GGVCFs changes to revert "no data" calls to "./." and change GQ0 hom-refs to no-calls #8741

ldgauthier · 2024-03-14T19:54:58Z

Several GQ0 cleanup changes:
Set GGVCFs --all-sites GQ0 hom-refs to no-calls
Set regular GGVCFs GQ0 hom-refs to no-calls (any DP, PL) for better AF/AN annotations
Remove PLs in "no data" case where DP=0 for more accurate QUAL score

Users can expect ANs to be reduced where GQ0 hom-refs previously occurred. QUALs may be decreased where PL=[0,0,0] because those genotypes are no longer included in QUAL calculations. QD will change where QUAL changes. InbreedingCoeff and ExcessHet will change because GQ0 hom-refs don't count anymore. None of these changes significantly impacted NA12878 accuracy in exome and WGS tests.

ldgauthier · 2024-03-15T13:55:26Z

...roadinstitute/hellbender/tools/walkers/GenotypeGVCFs/multiallelicQualRegression.expected.vcf

@@ -56,26 +56,26 @@
 ##source=GenomicsDBImport
 ##source=SelectVariants
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	CHMI_CHMI3_Nex1	NA12878	NA12891	NA12892	NA19238	NA20845	NA20846	NA20847	NA20849	NA20850	NA20851	NA20852	NA20853	NA20854	NA20856	NA20858	NA20859	NA20861	NA20862	NA20866	NA20869	NA20870	NA20871	NA20872	NA20873	NA20874	NA20875	NA20876	NA20877	NA20878	NA20881	NA20885	NA20886	NA20887	NA20888	NA20889	NA20890	NA20891	NA20892	NA20893	NA20894	NA20895	NA20896	NA20897	NA20898	NA20899	NA20901	NA20902	NA20903	NA20904	NA20905	NA20906	NA20908	NA20910	NA20911	NA21086	NA21087	NA21088	NA21093	NA21095	NA21114	NA21124	NA21126	NA21129	NA21137
-chr1	3836468	.	GTTTT	GTTTTT,GTTTTTTT,G,GTTTTTT	882.48	.	AC=3,2,1,3;AF=0.026,0.018,8.772e-03,0.026;AN=114;BaseQRankSum=0.00;DP=2100;ExcessHet=0.1247;FS=2.272;InbreedingCoeff=0.1698;MLEAC=2,2,1,3;MLEAF=0.018,0.018,8.772e-03,0.026;MQ=54.73;MQRankSum=0.00;QD=10.38;ReadPosRankSum=-2.300e-01;SOR=0.483	GT:AD:DP:GQ:PL	0/1:11,22,0,0,0:44:99:239,0,174,338,219,636,338,219,636,636,338,219,636,636,636	0/0:27,0,0,0,0:27:50	0/0:30,0,0,0,0:30:10	0/0:28,0,0,0,0:28:10	./.:3,0,0,0,0:3:0	0/0:27,0,0,0,0:27:60	0/0:59,0,0,0,0:59:30	0/2:3,0,7,0,0:10:59:132,142,223,0,80,59,142,223,80,223,142,223,80,223,223	0/0:33,0,0,0,0:33:60	0/0:31,0,0,0,0:31:60	.:0,0,0,0,0	0/0:27,0,0,0,0:27:60	0/0:30,0,0,0,0:30:60	0/0:51,0,0,0,0:51:40	0/0:29,0,0,0,0:29:60	0/0:31,0,0,0,0:31:60	0/3:8,0,0,4,0:14:99:103,160,534,160,534,534,0,437,437,670,160,534,534,437,534	0/0:30,0,0,0,0:30:60	0/0:32,0,0,0,0:32:60	0/0:37,0,0,0,0:37:60	0/0:49,0,0,0,0:49:40	0/0:36,0,0,0,0:36:60	0/2:2,0,2,0,0:4:34:34,42,113,0,71,65,42,113,71,113,42,113,71,113,113	0/0:10,0,0,0,0:14:29:0,29,176,29,176,176,29,176,176,176,29,176,176,176,176	0/0:58,0,0,0,0:58:30	0/0:32,0,0,0,0:32:60	0/0:11,0,0,0,0:13:34:0,34,285,34,285,285,34,285,285,285,34,285,285,285,285	0/0:26,0,0,0,0:26:60	0/0:26,0,0,0,0:26:60	0/0:32,0,0,0,0:32:60	.:0,0,0,0,0	0/0:29,0,0,0,0:29:60	0/4:1,0,0,0,6:11:35:94,175,487,175,487,487,175,487,487,487,0,90,90,90,35	0/0:40,0,0,0,0:40:10	0/0:41,0,0,0,0:41:60	0/0:30,0,0,0,0:30:60	0/4:2,0,0,0,9:11:10:186,193,234,193,234,234,193,234,234,234,0,41,41,41,10	0/0:43,0,0,0,0:43:20	0/4:0,0,0,0,6:8:11:123,146,198,146,198,198,146,198,198,198,0,24,24,24,11	0/0:28,0,0,0,0:28:10	0/0:29,0,0,0,0:29:60	.:0,0,0,0,0	0/0:30,0,0,0,0:30:60	0/0:10,0,0,0,0:14:88:0,88,622,88,622,622,88,622,622,622,88,622,622,622,622	0/0:34,0,0,0,0:34:30	0/0:23,0,0,0,0:23:50	0/0:37,0,0,0,0:37:50	0/0:29,0,0,0,0:29:60	0/0:34,0,0,0,0:34:30	0/0:43,0,0,0,0:43:20	.:0,0,0,0,0	0/0:31,0,0,0,0:31:60	0/0:39,0,0,0,0:39:60	0/0:28,0,0,0,0:28:60	0/0:36,0,0,0,0:36:60	0/0:38,0,0,0,0:38:60	0/0:36,0,0,0,0:36:30	0/0:31,0,0,0,0:31:50	0/0:29,0,0,0,0:29:50	.:0,0,0,0,0	0/0:33,0,0,0,0:33:60	.:0,0,0,0,0	1/1:0,2,0,0,0:2:8:47,8,0,47,8,47,47,8,47,47,47,8,47,47,47	0/0:15,0,0,0,0:15:10	.:0,0,0,0,0
+chr1	3836468	.	GTTTT	GTTTTT,GTTTTTTT,G,GTTTTTT	881.67	.	AC=3,2,1,3;AF=0.026,0.018,8.772e-03,0.026;AN=114;BaseQRankSum=0.00;DP=2100;ExcessHet=0.1247;FS=2.272;InbreedingCoeff=0.1698;MLEAC=2,2,1,3;MLEAF=0.018,0.018,8.772e-03,0.026;MQ=54.73;MQRankSum=0.00;QD=10.37;ReadPosRankSum=-2.300e-01;SOR=0.483	GT:AD:DP:GQ:PL	0/1:11,22,0,0,0:44:99:239,0,174,338,219,636,338,219,636,636,338,219,636,636,636	0/0:27,0,0,0,0:27:50	0/0:30,0,0,0,0:30:10	0/0:28,0,0,0,0:28:10	./.:3,0,0,0,0:3:0	0/0:27,0,0,0,0:27:60	0/0:59,0,0,0,0:59:30	0/2:3,0,7,0,0:10:59:132,142,223,0,80,59,142,223,80,223,142,223,80,223,223	0/0:33,0,0,0,0:33:60	0/0:31,0,0,0,0:31:60	.:0,0,0,0,0	0/0:27,0,0,0,0:27:60	0/0:30,0,0,0,0:30:60	0/0:51,0,0,0,0:51:40	0/0:29,0,0,0,0:29:60	0/0:31,0,0,0,0:31:60	0/3:8,0,0,4,0:14:99:103,160,534,160,534,534,0,437,437,670,160,534,534,437,534	0/0:30,0,0,0,0:30:60	0/0:32,0,0,0,0:32:60	0/0:37,0,0,0,0:37:60	0/0:49,0,0,0,0:49:40	0/0:36,0,0,0,0:36:60	0/2:2,0,2,0,0:4:34:34,42,113,0,71,65,42,113,71,113,42,113,71,113,113	0/0:10,0,0,0,0:14:29:0,29,176,29,176,176,29,176,176,176,29,176,176,176,176	0/0:58,0,0,0,0:58:30	0/0:32,0,0,0,0:32:60	0/0:11,0,0,0,0:13:34:0,34,285,34,285,285,34,285,285,285,34,285,285,285,285	0/0:26,0,0,0,0:26:60	0/0:26,0,0,0,0:26:60	0/0:32,0,0,0,0:32:60	.:0,0,0,0,0	0/0:29,0,0,0,0:29:60	0/4:1,0,0,0,6:11:35:94,175,487,175,487,487,175,487,487,487,0,90,90,90,35	0/0:40,0,0,0,0:40:10	0/0:41,0,0,0,0:41:60	0/0:30,0,0,0,0:30:60	0/4:2,0,0,0,9:11:10:186,193,234,193,234,234,193,234,234,234,0,41,41,41,10	0/0:43,0,0,0,0:43:20	0/4:0,0,0,0,6:8:11:123,146,198,146,198,198,146,198,198,198,0,24,24,24,11	0/0:28,0,0,0,0:28:10	0/0:29,0,0,0,0:29:60	.:0,0,0,0,0	0/0:30,0,0,0,0:30:60	0/0:10,0,0,0,0:14:88:0,88,622,88,622,622,88,622,622,622,88,622,622,622,622	0/0:34,0,0,0,0:34:30	0/0:23,0,0,0,0:23:50	0/0:37,0,0,0,0:37:50	0/0:29,0,0,0,0:29:60	0/0:34,0,0,0,0:34:30	0/0:43,0,0,0,0:43:20	.:0,0,0,0,0	0/0:31,0,0,0,0:31:60	0/0:39,0,0,0,0:39:60	0/0:28,0,0,0,0:28:60	0/0:36,0,0,0,0:36:60	0/0:38,0,0,0,0:38:60	0/0:36,0,0,0,0:36:30	0/0:31,0,0,0,0:31:50	0/0:29,0,0,0,0:29:50	.:0,0,0,0,0	0/0:33,0,0,0,0:33:60	.:0,0,0,0,0	1/1:0,2,0,0,0:2:8:47,8,0,47,8,47,47,8,47,47,47,8,47,47,47	0/0:15,0,0,0,0:15:10	.:0,0,0,0,0


QUAL changed, so QD changed. I'm honestly not sure why QUAL changed when the PLs are all the same... I think the new one is correct because the old QUAL was the same in the previous PR with AN=116

ldgauthier · 2024-03-15T13:57:20Z

...nder/tools/walkers/GenotypeGVCFs/expected/gvcf.basepairResolution.includeNonVariantSites.vcf

@@ -1550,7 +1550,7 @@
 20	10001434	.	G	.	.	.	DP=44	GT:AD:DP:RGQ	0/0:44:44:18
 20	10001435	.	A	.	.	.	DP=44	GT:AD:DP:RGQ	0/0:38:44:0
 20	10001436	.	A	AAGGCT	1872.03	.	AC=2;AF=1.00;AN=2;DP=43;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=220.07;MQ0=0;QD=25.36;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,42:42:99:1886,125,0
-20	10001437	.	A	.	.	.	DP=44	GT:AD:DP:RGQ	0/0:2:44:0
+20	10001437	.	A	.	.	.	DP=44	GT:AD:DP:RGQ	./.:2:44:0


Mission accomplished

droazen · 2024-03-15T17:20:53Z

@ldgauthier Is this one ready for review?

ldgauthier · 2024-04-02T14:09:36Z

src/test/java/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFsIntegrationTest.java

                //combine not supported yet, see https://github.com/broadinstitute/gatk/issues/2429 and https://github.com/broadinstitute/gatk/issues/2584
                //{"combine.single.sample.pipeline.1.vcf", null, Arrays.asList("-V", getTestFile("combine.single.sample.pipeline.2.vcf").toString() , "-V", getTestFile("combine.single.sample.pipeline.3.vcf").toString()), b37_reference_20_21},
-                /*
+


Reenable tests -- oops

ldgauthier · 2024-04-02T14:10:13Z

src/test/java/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFsIntegrationTest.java

-        Assert.assertEquals(g.getAD(), new int[2]);
-        Assert.assertTrue(g.hasPL());
-        Assert.assertEquals(g.getPL(), new int[3]);
+        Assert.assertFalse(g.hasGQ());


These are "no data" no calls that we're going to change to ./.

ldgauthier · 2024-04-02T14:10:18Z

src/test/java/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFsIntegrationTest.java

-        Assert.assertTrue(g.hasDP());
-        Assert.assertEquals(g.getDP(), 0);
-        Assert.assertTrue(g.hasAD());  //this is different from Gnarly behavior
+        Assert.assertFalse(g.hasGQ());


These are "no data" no calls that we're going to change to ./.

ldgauthier · 2024-04-02T14:10:27Z

src/test/java/org/broadinstitute/hellbender/tools/walkers/GnarlyGenotyperIntegrationTest.java

-        Assert.assertEquals(g.getGQ(), 0);
-        Assert.assertTrue(g.hasDP());
-        Assert.assertEquals(g.getDP(), 0);
+        Assert.assertFalse(g.hasGQ());


These are "no data" no calls that we're going to change to ./.

ldgauthier · 2024-04-02T14:12:52Z

...itute/hellbender/tools/walkers/GenotypeGVCFs/chr21.bad.pl.gatk3.7_30_ga4f720357.expected.vcf

@@ -3401,4 +3401,4 @@
 ##contig=<ID=HLA-DRB1*16:02:01,length=11005>
 ##source=SelectVariants
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HG00096	HG00268	HG00419	HG00759	HG01051	HG01112	HG01500	HG01565	HG01583	HG01595	HG01879	HG02568	HG02922	HG03006	HG03052	HG03642	HG03742	NA18525	NA18939	NA19017	NA19625	NA19648	NA20502	NA20845
-chr21	28341778	.	G	A	479.87	.	AC=1;AF=0.022;AN=46;BaseQRankSum=1.12;ClippingRankSum=0.329;DP=914;ExcessHet=0.0000;FS=6.865;InbreedingCoeff=0.1268;MLEAC=1;MLEAF=0.022;MQ=59.29;MQRankSum=0.152;QD=9.79;RAW_MQ=298800.00;ReadPosRankSum=-2.530e-01;SOR=0.236	GT:AD:DP:GQ:PL	0/0:35,0:35:99:0,99,1210	0/0:44,0:44:99:0,105,1317	0/0:43,0:43:0:0,0,83	0/0:54,0:54:0:0,0,524	0/0:34,0:34:99:0,99,1061	0/0:44,0:44:99:0,107,1464	0/0:38,0:38:99:0,101,1138	0/0:32,0:34:94:0,94,831	0/0:40,0:40:99:0,103,1210	0/0:36,0:36:99:0,103,1055	0/0:39,0:39:99:0,104,1179	0/0:17,0:17:51:0,51,471	0/0:39,0:39:99:0,110,1170	0/0:35,0:35:99:0,105,1040	0/0:36,0:36:99:0,99,1030	0/0:32,0:32:0:0,0,266	0/0:43,0:43:99:0,100,1295	0/0:35,0:35:99:0,105,1071	0/0:34,0:34:99:0,99,1056	0/0:34,0:34:99:0,102,1031	./.:36,0:36:0:0,0,0	0/1:28,21:49:99:493,0,646	0/0:42,0:42:99:0,101,1499	0/0:41,0:41:99:0,103,1368
+chr21	28341778	.	G	A	479.87	.	AC=1;AF=0.025;AN=40;BaseQRankSum=1.12;ClippingRankSum=0.329;DP=914;ExcessHet=0.0000;FS=6.865;InbreedingCoeff=0.1268;MLEAC=1;MLEAF=0.025;MQ=37.37;MQRankSum=0.152;QD=9.79;RAW_MQ=298800.00;ReadPosRankSum=-2.530e-01;SOR=0.236	GT:AD:DP:GQ:PL	0/0:35,0:35:99:0,99,1210	0/0:44,0:44:99:0,105,1317	./.:43,0:43:0:0,0,83	./.:54,0:54:0:0,0,524	0/0:34,0:34:99:0,99,1061	0/0:44,0:44:99:0,107,1464	0/0:38,0:38:99:0,101,1138	0/0:32,0:34:94:0,94,831	0/0:40,0:40:99:0,103,1210	0/0:36,0:36:99:0,103,1055	0/0:39,0:39:99:0,104,1179	0/0:17,0:17:51:0,51,471	0/0:39,0:39:99:0,110,1170	0/0:35,0:35:99:0,105,1040	0/0:36,0:36:99:0,99,1030	./.:32,0:32:0:0,0,266	0/0:43,0:43:99:0,100,1295	0/0:35,0:35:99:0,105,1071	0/0:34,0:34:99:0,99,1056	0/0:34,0:34:99:0,102,1031	./.:36,0:36:0:0,0,0	0/1:28,21:49:99:493,0,646	0/0:42,0:42:99:0,101,1499	0/0:41,0:41:99:0,103,1368


GQ0 hom-refs go to no-call so we can get better AF and AN values

ldgauthier · 2024-04-02T14:13:35Z

...ools/walkers/GenotypeGVCFs/combined_genotype_gvcf_exception.gatk3.7_30_ga4f720357.output.vcf

@@ -117,4 +119,4 @@
 ##reference=file:///seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta
 ##source=SelectVariants
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	Sample_0	Sample_1	Sample_10	Sample_100	Sample_101	Sample_102	Sample_103	Sample_104	Sample_105	Sample_106	Sample_107	Sample_108	Sample_109	Sample_11	Sample_110	Sample_111	Sample_112	Sample_113	Sample_114	Sample_115	Sample_116	Sample_117	Sample_118	Sample_119	Sample_12	Sample_120	Sample_121	Sample_122	Sample_123	Sample_124	Sample_125	Sample_126	Sample_127	Sample_128	Sample_129	Sample_13	Sample_130	Sample_131	Sample_132	Sample_133	Sample_134	Sample_135	Sample_136	Sample_137	Sample_138	Sample_139	Sample_14	Sample_140	Sample_141	Sample_142	Sample_143	Sample_144	Sample_145	Sample_146	Sample_147	Sample_148	Sample_149	Sample_15	Sample_150	Sample_151	Sample_152	Sample_153	Sample_154	Sample_155	Sample_156	Sample_157	Sample_158	Sample_159	Sample_16	Sample_160	Sample_161	Sample_162	Sample_163	Sample_164	Sample_165	Sample_166	Sample_167	Sample_168	Sample_169	Sample_17	Sample_170	Sample_171	Sample_172	Sample_173	Sample_174	Sample_175	Sample_176	Sample_177	Sample_178	Sample_179	Sample_18	Sample_180	Sample_181	Sample_182	Sample_183	Sample_184	Sample_185	Sample_186	Sample_187	Sample_188	Sample_189	Sample_19	Sample_190	Sample_191	Sample_192	Sample_193	Sample_194	Sample_195	Sample_196	Sample_197	Sample_198	Sample_199	Sample_2	Sample_20	Sample_200	Sample_201	Sample_202	Sample_203	Sample_204	Sample_205	Sample_206	Sample_207	Sample_208	Sample_209	Sample_21	Sample_210	Sample_211	Sample_212	Sample_213	Sample_214	Sample_215	Sample_216	Sample_217	Sample_218	Sample_219	Sample_22	Sample_220	Sample_221	Sample_222	Sample_223	Sample_224	Sample_225	Sample_226	Sample_227	Sample_228	Sample_229	Sample_23	Sample_230	Sample_231	Sample_232	Sample_233	Sample_234	Sample_235	Sample_236	Sample_237	Sample_238	Sample_239	Sample_24	Sample_240	Sample_241	Sample_242	Sample_243	Sample_244	Sample_245	Sample_246	Sample_247	Sample_248	Sample_249	Sample_25	Sample_250	Sample_251	Sample_252	Sample_253	Sample_254	Sample_255	Sample_256	Sample_257	Sample_258	Sample_259	Sample_26	Sample_260	Sample_261	Sample_262	Sample_263	Sample_264	Sample_265	Sample_266	Sample_267	Sample_268	Sample_269	Sample_27	Sample_270	Sample_271	Sample_272	Sample_273	Sample_274	Sample_275	Sample_276	Sample_277	Sample_278	Sample_279	Sample_28	Sample_280	Sample_281	Sample_282	Sample_283	Sample_284	Sample_285	Sample_286	Sample_287	Sample_288	Sample_289	Sample_29	Sample_290	Sample_291	Sample_292	Sample_293	Sample_294	Sample_295	Sample_296	Sample_297	Sample_298	Sample_3	Sample_30	Sample_31	Sample_32	Sample_33	Sample_34	Sample_35	Sample_36	Sample_37	Sample_38	Sample_39	Sample_4	Sample_40	Sample_41	Sample_42	Sample_43	Sample_44	Sample_45	Sample_46	Sample_47	Sample_48	Sample_49	Sample_5	Sample_50	Sample_51	Sample_52	Sample_53	Sample_54	Sample_55	Sample_56	Sample_57	Sample_58	Sample_59	Sample_6	Sample_60	Sample_61	Sample_62	Sample_63	Sample_64	Sample_65	Sample_66	Sample_67	Sample_68	Sample_69	Sample_7	Sample_70	Sample_71	Sample_72	Sample_73	Sample_74	Sample_75	Sample_76	Sample_77	Sample_78	Sample_79	Sample_8	Sample_80	Sample_81	Sample_82	Sample_83	Sample_84	Sample_85	Sample_86	Sample_87	Sample_88	Sample_89	Sample_9	Sample_90	Sample_91	Sample_92	Sample_93	Sample_94	Sample_95	Sample_96	Sample_97	Sample_98	Sample_99
-20	1115540	.	AC	A	557.01	.	AC=3;AF=5.017e-03;AN=598;BaseQRankSum=-3.770e-01;DP=3640;ExcessHet=0.0220;FS=0.000;InbreedingCoeff=-0.0217;MLEAC=3;MLEAF=5.017e-03;MQ=59.68;MQ0=0;MQRankSum=1.00;QD=12.38;ReadPosRankSum=0.462;SOR=0.760	GT:AD:DP:GQ:PL	0/0:12,0:12:36:0,36,406	0/0:12,0:12:31:0,31,464	0/0:8,0:8:18:0,18,270	0/0:10,0:10:21:0,21,315	0/0:5,0:5:15:0,15,211	0/0:7,0:7:21:0,21,242	0/0:22,0:22:60:0,60,678	0/0:12,0:12:28:0,28,423	0/0:7,0:7:21:0,21,213	0/0:9,0:9:21:0,21,315	0/0:10,0:10:30:0,30,335	0/0:8,0:8:21:0,21,315	0/0:24,0:24:60:0,60,823	0/0:6,0:6:12:0,12,164	0/0:12,0:12:27:0,27,396	0/0:2,0:2:6:0,6,64	0/0:9,0:9:21:0,21,308	0/0:21,0:21:60:0,60,900	0/0:23,0:23:60:0,60,750	0/0:9,0:9:21:0,21,312	0/0:5,0:5:9:0,9,135	0/0:12,0:12:24:0,24,360	0/0:7,0:7:21:0,21,249	0/0:10,0:10:21:0,21,312	0/0:10,0:10:21:0,21,315	0/0:10,0:10:21:0,21,315	0/0:7,0:7:21:0,21,222	0/0:9,0:9:14:0,14,212	0/0:14,0:14:36:0,36,464	0/0:25,0:25:69:0,69,1035	0/0:9,0:9:21:0,21,315	0/0:9,0:9:24:0,24,360	0/0:5,0:5:12:0,12,158	0/0:21,0:21:60:0,60,900	0/0:11,0:11:21:0,21,315	0/0:9,0:9:21:0,21,281	0/0:10,0:10:18:0,18,270	0/0:8,0:8:21:0,21,272	0/0:8,0:8:20:0,20,254	0/0:11,0:11:21:0,21,315	0/0:5,0:5:12:0,12,180	0/0:7,0:7:21:0,21,260	0/0:2,0:2:6:0,6,70	0/0:23,0:23:60:0,60,807	0/0:4,0:4:6:0,6,90	0/0:10,0:10:27:0,27,323	0/0:7,0:7:21:0,21,220	0/0:11,0:11:21:0,21,315	0/0:13,0:13:26:0,26,417	0/0:6,0:6:9:0,9,135	0/0:6,0:6:18:0,18,185	0/0:6,0:6:0:0,0,96	0/0:7,0:7:21:0,21,252	0/0:9,0:9:21:0,21,315	0/0:2,0:2:6:0,6,68	0/0:9,0:9:24:0,24,309	0/0:3,0:3:6:0,6,90	0/0:11,0:11:24:0,24,347	0/0:8,0:8:21:0,21,264	0/0:8,0:8:21:0,21,315	0/0:22,0:22:60:0,60,900	0/0:31,0:31:81:0,81,1215	0/0:24,0:24:60:0,60,900	0/0:17,0:17:26:0,26,578	0/0:13,0:13:19:0,19,401	0/0:9,0:9:24:0,24,295	0/0:22,0:22:60:0,60,770	0/0:24,0:24:63:0,63,945	0/0:8,0:8:21:0,21,315	0/0:7,0:7:18:0,18,270	0/0:8,0:8:21:0,21,272	0/0:6,0:6:18:0,18,201	0/0:5,0:5:15:0,15,154	0/0:24,0:24:60:0,60,900	0/0:25,0:25:60:0,60,900	0/0:7,0:7:21:0,21,281	0/0:2,0:2:6:0,6,74	0/0:19,0:19:42:0,42,630	0/0:22,0:22:60:0,60,890	0/0:9,0:9:21:0,21,315	0/0:25,0:25:60:0,60,882	0/0:24,0:24:60:0,60,900	0/0:3,0:3:6:0,6,96	0/0:7,0:7:21:0,21,242	0/0:7,0:7:21:0,21,293	0/0:9,0:9:27:0,27,294	0/0:3,0:3:9:0,9,98	0/0:9,0:9:21:0,21,315	0/0:6,0:6:18:0,18,182	0/0:8,0:8:12:0,12,216	0/0:9,0:9:21:0,21,315	0/0:6,0:6:12:0,12,180	0/0:7,0:7:18:0,18,270	0/0:7,0:7:21:0,21,222	0/0:4,0:4:6:0,6,90	0/0:7,0:7:21:0,21,245	0/0:6,0:6:15:0,15,178	0/0:4,0:4:6:0,6,90	0/0:9,0:9:21:0,21,276	0/0:8,0:8:21:0,21,315	0/0:5,0:5:9:0,9,135	0/0:24,0:24:60:0,60,900	0/0:3,0:3:6:0,6,90	0/0:3,0:3:9:0,9,109	0/0:7,0:7:21:0,21,240	0/0:5,0:5:12:0,12,180	0/0:29,0:29:75:0,75,1125	0/0:8,0:8:21:0,21,315	0/0:14,0:14:30:0,30,450	0/0:10,0:10:24:0,24,360	0/0:7,0:7:21:0,21,210	0/0:16,0:16:39:0,39,540	0/0:12,0:12:23:0,23,401	0/0:5,0:5:9:0,9,135	0/0:20,0:20:52:0,52,695	0/0:25,0:25:60:0,60,900	0/0:9,0:9:21:0,21,284	0/0:9,0:9:24:0,24,360	0/0:18,0:18:51:0,51,596	0/0:14,0:14:27:0,27,405	0/0:15,0:15:39:0,39,579	0/0:22,0:22:60:0,60,729	0/0:8,0:8:21:0,21,308	0/0:13,0:13:26:0,26,450	0/0:19,0:19:36:0,36,628	0/1:12,11:23:99:291,0,321	0/0:15,0:15:24:0,24,450	0/0:10,0:10:21:0,21,315	0/0:11,0:11:33:0,33,408	0/0:21,0:21:51:0,51,765	0/0:15,0:15:20:0,20,540	0/0:12,0:12:27:0,27,405	0/0:9,0:9:21:0,21,315	0/0:12,0:12:27:0,27,405	0/0:22,0:22:60:0,60,900	0/0:8,0:8:21:0,21,295	0/0:2,0:2:6:0,6,64	0/0:14,0:14:28:0,28,437	0/0:2,0:2:6:0,6,76	0/0:27,0:27:60:0,60,900	0/0:9,0:9:13:0,13,243	0/0:6,0:6:12:0,12,180	0/0:9,0:9:21:0,21,296	0/0:11,0:11:30:0,30,343	0/0:6,0:6:18:0,18,216	0/0:24,0:24:61:0,61,945	0/0:14,0:14:27:0,27,405	0/0:5,0:5:9:0,9,135	0/0:5,0:5:9:0,9,135	0/0:10,0:10:21:0,21,360	0/0:7,0:7:21:0,21,235	0/0:2,0:2:6:0,6,65	0/0:3,0:3:6:0,6,90	0/0:25,0:25:60:0,60,900	0/0:14,0:14:22:0,22,532	0/0:4,0:4:6:0,6,90	0/0:8,0:8:21:0,21,273	0/0:24,0:24:63:0,63,945	0/0:2,0:2:6:0,6,67	0/0:18,0:18:33:0,33,495	0/0:8,0:8:21:0,21,238	0/0:11,0:11:24:0,24,320	0/0:23,0:23:60:0,60,900	0/0:23,0:23:60:0,60,900	0/0:9,0:9:21:0,21,315	0/0:10,0:10:24:0,24,360	0/0:22,0:22:60:0,60,772	0/0:8,0:8:20:0,20,315	0/0:22,0:22:60:0,60,900	0/0:21,0:21:60:0,60,657	0/0:13,0:13:22:0,22,450	0/0:7,0:7:21:0,21,253	0/0:9,0:9:20:0,20,322	0/0:4,0:4:12:0,12,147	0/0:9,0:9:27:0,27,302	0/0:3,0:3:6:0,6,90	0/0:7,0:7:21:0,21,281	0/0:7,0:7:21:0,21,261	0/0:10,0:10:24:0,24,360	0/0:10,0:10:24:0,24,360	0/0:8,0:8:21:0,21,315	0/0:9,0:9:24:0,24,318	0/0:24,0:24:60:0,60,900	0/0:26,0:26:63:0,63,945	0/0:8,0:8:21:0,21,283	0/1:3,6:9:70:169,0,70	0/0:8,0:8:21:0,21,315	0/0:2,0:2:6:0,6,62	0/0:8,0:8:21:0,21,247	0/0:3,0:3:6:0,6,87	0/0:23,0:23:60:0,60,900	0/0:2,0:2:6:0,6,67	0/0:5,0:5:6:0,6,90	0/0:3,0:3:6:0,6,90	0/0:8,0:8:21:0,21,285	0/0:8,0:8:18:0,18,270	0/0:5,0:5:9:0,9,135	0/0:9,0:9:21:0,21,315	0/0:22,0:22:60:0,60,900	0/0:9,0:9:21:0,21,315	0/0:8,0:8:24:0,24,258	0/0:9,0:9:24:0,24,360	0/0:5,0:5:3:0,3,125	0/0:8,0:8:21:0,21,231	0/0:6,0:6:15:0,15,225	0/0:3,0:3:6:0,6,90	0/0:7,0:7:21:0,21,219	0/0:5,0:5:12:0,12,158	0/0:4,0:4:9:0,9,130	0/0:7,0:7:21:0,21,237	0/0:26,0:26:60:0,60,895	0/0:24,0:24:60:0,60,850	0/0:7,0:7:21:0,21,272	0/0:8,0:8:22:0,22,330	0/0:28,0:28:67:0,67,1080	0/0:22,0:22:26:0,26,683	0/0:11,0:11:24:0,24,360	0/0:26,0:26:63:0,63,894	0/0:22,0:22:60:0,60,900	0/0:9,0:9:21:0,21,315	0/0:19,0:19:22:0,22,686	0/0:25,0:25:60:0,60,900	0/0:25,0:25:57:0,57,855	0/0:8,0:8:21:0,21,279	0/0:27,0:27:63:0,63,945	0/0:26,0:26:63:0,63,898	0/0:9,0:9:21:0,21,315	0/0:8,0:8:21:0,21,315	0/0:11,0:11:21:0,21,315	0/0:21,0:21:60:0,60,707	0/0:8,0:8:21:0,21,315	0/0:10,0:10:3:0,3,244	0/0:25,0:25:63:0,63,935	0/0:4,0:4:12:0,12,146	0/0:23,0:23:60:0,60,900	0/0:9,0:9:0:0,0,237	0/0:23,0:23:60:0,60,900	0/0:18,0:18:42:0,42,615	0/0:9,0:9:21:0,21,315	0/0:19,0:19:45:0,45,627	0/0:9,0:9:21:0,21,315	0/0:23,0:23:50:0,50,670	0/0:13,0:13:23:0,23,405	0/0:10,0:10:21:0,21,315	0/0:8,0:8:21:0,21,315	0/0:2,0:2:6:0,6,71	0/0:10,0:10:27:0,27,403	0/0:8,0:8:21:0,21,315	0/0:7,0:7:10:0,10,253	0/0:4,0:4:9:0,9,135	0/0:21,0:21:60:0,60,900	0/0:10,0:10:21:0,21,315	0/0:7,0:7:21:0,21,190	0/0:12,0:12:33:0,33,458	0/0:13,0:13:30:0,30,450	0/0:8,0:8:21:0,21,315	0/0:14,0:14:24:0,24,360	0/0:6,0:6:15:0,15,175	0/0:22,0:22:60:0,60,658	0/0:11,0:11:21:0,21,315	0/0:8,0:8:21:0,21,315	0/0:11,0:11:27:0,27,405	0/0:13,0:13:27:0,27,405	0/0:10,0:10:21:0,21,315	0/0:26,0:26:60:0,60,900	0/0:21,0:21:63:0,63,700	0/0:19,0:19:57:0,57,594	0/0:22,0:22:60:0,60,900	0/0:25,0:25:63:0,63,945	0/0:23,0:23:69:0,69,752	0/0:15,0:15:36:0,36,540	0/0:8,0:8:21:0,21,273	0/0:27,0:27:63:0,63,945	0/0:7,0:7:21:0,21,234	0/0:12,0:12:29:0,29,361	0/0:14,0:14:30:0,30,450	0/0:12,0:12:24:0,24,360	0/0:8,0:8:21:0,21,290	0/0:27,0:27:60:0,60,900	0/0:10,0:10:21:0,21,315	0/0:23,0:23:60:0,60,900	0/0:21,0:21:48:0,48,720	0/0:8,0:8:21:0,21,261	0/0:9,0:9:21:0,21,315	0/0:9,0:9:21:0,21,315	0/0:20,0:20:60:0,60,614	0/0:15,0:15:22:0,22,495	0/0:11,0:11:21:0,21,315	0/0:20,0:20:51:0,51,765	0/0:13,0:13:27:0,27,405	0/0:21,0:21:60:0,60,900	0/0:24,0:24:60:0,60,900	0/0:23,0:23:60:0,60,870	0/1:7,6:13:99:156,0,188	0/0:13,0:13:27:0,27,405	0/0:24,0:24:60:0,60,900	0/0:8,0:8:21:0,21,315	0/0:7,0:7:21:0,21,241	0/0:16,0:16:30:0,30,450
+20	1115540	.	AC	A	557.01	.	AC=3;AF=5.051e-03;AN=594;BaseQRankSum=-3.770e-01;DP=3640;ExcessHet=0.0220;FS=0.000;InbreedingCoeff=-0.0217;MLEAC=3;MLEAF=5.051e-03;MQ=59.68;MQ0=0;MQRankSum=1.00;QD=12.38;ReadPosRankSum=0.462;SOR=0.760	GT:AD:DP:GQ:PL	0/0:12,0:12:36:0,36,406	0/0:12,0:12:31:0,31,464	0/0:8,0:8:18:0,18,270	0/0:10,0:10:21:0,21,315	0/0:5,0:5:15:0,15,211	0/0:7,0:7:21:0,21,242	0/0:22,0:22:60:0,60,678	0/0:12,0:12:28:0,28,423	0/0:7,0:7:21:0,21,213	0/0:9,0:9:21:0,21,315	0/0:10,0:10:30:0,30,335	0/0:8,0:8:21:0,21,315	0/0:24,0:24:60:0,60,823	0/0:6,0:6:12:0,12,164	0/0:12,0:12:27:0,27,396	0/0:2,0:2:6:0,6,64	0/0:9,0:9:21:0,21,308	0/0:21,0:21:60:0,60,900	0/0:23,0:23:60:0,60,750	0/0:9,0:9:21:0,21,312	0/0:5,0:5:9:0,9,135	0/0:12,0:12:24:0,24,360	0/0:7,0:7:21:0,21,249	0/0:10,0:10:21:0,21,312	0/0:10,0:10:21:0,21,315	0/0:10,0:10:21:0,21,315	0/0:7,0:7:21:0,21,222	0/0:9,0:9:14:0,14,212	0/0:14,0:14:36:0,36,464	0/0:25,0:25:69:0,69,1035	0/0:9,0:9:21:0,21,315	0/0:9,0:9:24:0,24,360	0/0:5,0:5:12:0,12,158	0/0:21,0:21:60:0,60,900	0/0:11,0:11:21:0,21,315	0/0:9,0:9:21:0,21,281	0/0:10,0:10:18:0,18,270	0/0:8,0:8:21:0,21,272	0/0:8,0:8:20:0,20,254	0/0:11,0:11:21:0,21,315	0/0:5,0:5:12:0,12,180	0/0:7,0:7:21:0,21,260	0/0:2,0:2:6:0,6,70	0/0:23,0:23:60:0,60,807	0/0:4,0:4:6:0,6,90	0/0:10,0:10:27:0,27,323	0/0:7,0:7:21:0,21,220	0/0:11,0:11:21:0,21,315	0/0:13,0:13:26:0,26,417	0/0:6,0:6:9:0,9,135	0/0:6,0:6:18:0,18,185	./.:6,0:6:0:0,0,96	0/0:7,0:7:21:0,21,252	0/0:9,0:9:21:0,21,315	0/0:2,0:2:6:0,6,68	0/0:9,0:9:24:0,24,309	0/0:3,0:3:6:0,6,90	0/0:11,0:11:24:0,24,347	0/0:8,0:8:21:0,21,264	0/0:8,0:8:21:0,21,315	0/0:22,0:22:60:0,60,900	0/0:31,0:31:81:0,81,1215	0/0:24,0:24:60:0,60,900	0/0:17,0:17:26:0,26,578	0/0:13,0:13:19:0,19,401	0/0:9,0:9:24:0,24,295	0/0:22,0:22:60:0,60,770	0/0:24,0:24:63:0,63,945	0/0:8,0:8:21:0,21,315	0/0:7,0:7:18:0,18,270	0/0:8,0:8:21:0,21,272	0/0:6,0:6:18:0,18,201	0/0:5,0:5:15:0,15,154	0/0:24,0:24:60:0,60,900	0/0:25,0:25:60:0,60,900	0/0:7,0:7:21:0,21,281	0/0:2,0:2:6:0,6,74	0/0:19,0:19:42:0,42,630	0/0:22,0:22:60:0,60,890	0/0:9,0:9:21:0,21,315	0/0:25,0:25:60:0,60,882	0/0:24,0:24:60:0,60,900	0/0:3,0:3:6:0,6,96	0/0:7,0:7:21:0,21,242	0/0:7,0:7:21:0,21,293	0/0:9,0:9:27:0,27,294	0/0:3,0:3:9:0,9,98	0/0:9,0:9:21:0,21,315	0/0:6,0:6:18:0,18,182	0/0:8,0:8:12:0,12,216	0/0:9,0:9:21:0,21,315	0/0:6,0:6:12:0,12,180	0/0:7,0:7:18:0,18,270	0/0:7,0:7:21:0,21,222	0/0:4,0:4:6:0,6,90	0/0:7,0:7:21:0,21,245	0/0:6,0:6:15:0,15,178	0/0:4,0:4:6:0,6,90	0/0:9,0:9:21:0,21,276	0/0:8,0:8:21:0,21,315	0/0:5,0:5:9:0,9,135	0/0:24,0:24:60:0,60,900	0/0:3,0:3:6:0,6,90	0/0:3,0:3:9:0,9,109	0/0:7,0:7:21:0,21,240	0/0:5,0:5:12:0,12,180	0/0:29,0:29:75:0,75,1125	0/0:8,0:8:21:0,21,315	0/0:14,0:14:30:0,30,450	0/0:10,0:10:24:0,24,360	0/0:7,0:7:21:0,21,210	0/0:16,0:16:39:0,39,540	0/0:12,0:12:23:0,23,401	0/0:5,0:5:9:0,9,135	0/0:20,0:20:52:0,52,695	0/0:25,0:25:60:0,60,900	0/0:9,0:9:21:0,21,284	0/0:9,0:9:24:0,24,360	0/0:18,0:18:51:0,51,596	0/0:14,0:14:27:0,27,405	0/0:15,0:15:39:0,39,579	0/0:22,0:22:60:0,60,729	0/0:8,0:8:21:0,21,308	0/0:13,0:13:26:0,26,450	0/0:19,0:19:36:0,36,628	0/1:12,11:23:99:291,0,321	0/0:15,0:15:24:0,24,450	0/0:10,0:10:21:0,21,315	0/0:11,0:11:33:0,33,408	0/0:21,0:21:51:0,51,765	0/0:15,0:15:20:0,20,540	0/0:12,0:12:27:0,27,405	0/0:9,0:9:21:0,21,315	0/0:12,0:12:27:0,27,405	0/0:22,0:22:60:0,60,900	0/0:8,0:8:21:0,21,295	0/0:2,0:2:6:0,6,64	0/0:14,0:14:28:0,28,437	0/0:2,0:2:6:0,6,76	0/0:27,0:27:60:0,60,900	0/0:9,0:9:13:0,13,243	0/0:6,0:6:12:0,12,180	0/0:9,0:9:21:0,21,296	0/0:11,0:11:30:0,30,343	0/0:6,0:6:18:0,18,216	0/0:24,0:24:61:0,61,945	0/0:14,0:14:27:0,27,405	0/0:5,0:5:9:0,9,135	0/0:5,0:5:9:0,9,135	0/0:10,0:10:21:0,21,360	0/0:7,0:7:21:0,21,235	0/0:2,0:2:6:0,6,65	0/0:3,0:3:6:0,6,90	0/0:25,0:25:60:0,60,900	0/0:14,0:14:22:0,22,532	0/0:4,0:4:6:0,6,90	0/0:8,0:8:21:0,21,273	0/0:24,0:24:63:0,63,945	0/0:2,0:2:6:0,6,67	0/0:18,0:18:33:0,33,495	0/0:8,0:8:21:0,21,238	0/0:11,0:11:24:0,24,320	0/0:23,0:23:60:0,60,900	0/0:23,0:23:60:0,60,900	0/0:9,0:9:21:0,21,315	0/0:10,0:10:24:0,24,360	0/0:22,0:22:60:0,60,772	0/0:8,0:8:20:0,20,315	0/0:22,0:22:60:0,60,900	0/0:21,0:21:60:0,60,657	0/0:13,0:13:22:0,22,450	0/0:7,0:7:21:0,21,253	0/0:9,0:9:20:0,20,322	0/0:4,0:4:12:0,12,147	0/0:9,0:9:27:0,27,302	0/0:3,0:3:6:0,6,90	0/0:7,0:7:21:0,21,281	0/0:7,0:7:21:0,21,261	0/0:10,0:10:24:0,24,360	0/0:10,0:10:24:0,24,360	0/0:8,0:8:21:0,21,315	0/0:9,0:9:24:0,24,318	0/0:24,0:24:60:0,60,900	0/0:26,0:26:63:0,63,945	0/0:8,0:8:21:0,21,283	0/1:3,6:9:70:169,0,70	0/0:8,0:8:21:0,21,315	0/0:2,0:2:6:0,6,62	0/0:8,0:8:21:0,21,247	0/0:3,0:3:6:0,6,87	0/0:23,0:23:60:0,60,900	0/0:2,0:2:6:0,6,67	0/0:5,0:5:6:0,6,90	0/0:3,0:3:6:0,6,90	0/0:8,0:8:21:0,21,285	0/0:8,0:8:18:0,18,270	0/0:5,0:5:9:0,9,135	0/0:9,0:9:21:0,21,315	0/0:22,0:22:60:0,60,900	0/0:9,0:9:21:0,21,315	0/0:8,0:8:24:0,24,258	0/0:9,0:9:24:0,24,360	0/0:5,0:5:3:0,3,125	0/0:8,0:8:21:0,21,231	0/0:6,0:6:15:0,15,225	0/0:3,0:3:6:0,6,90	0/0:7,0:7:21:0,21,219	0/0:5,0:5:12:0,12,158	0/0:4,0:4:9:0,9,130	0/0:7,0:7:21:0,21,237	0/0:26,0:26:60:0,60,895	0/0:24,0:24:60:0,60,850	0/0:7,0:7:21:0,21,272	0/0:8,0:8:22:0,22,330	0/0:28,0:28:67:0,67,1080	0/0:22,0:22:26:0,26,683	0/0:11,0:11:24:0,24,360	0/0:26,0:26:63:0,63,894	0/0:22,0:22:60:0,60,900	0/0:9,0:9:21:0,21,315	0/0:19,0:19:22:0,22,686	0/0:25,0:25:60:0,60,900	0/0:25,0:25:57:0,57,855	0/0:8,0:8:21:0,21,279	0/0:27,0:27:63:0,63,945	0/0:26,0:26:63:0,63,898	0/0:9,0:9:21:0,21,315	0/0:8,0:8:21:0,21,315	0/0:11,0:11:21:0,21,315	0/0:21,0:21:60:0,60,707	0/0:8,0:8:21:0,21,315	0/0:10,0:10:3:0,3,244	0/0:25,0:25:63:0,63,935	0/0:4,0:4:12:0,12,146	0/0:23,0:23:60:0,60,900	./.:9,0:9:0:0,0,237	0/0:23,0:23:60:0,60,900	0/0:18,0:18:42:0,42,615	0/0:9,0:9:21:0,21,315	0/0:19,0:19:45:0,45,627	0/0:9,0:9:21:0,21,315	0/0:23,0:23:50:0,50,670	0/0:13,0:13:23:0,23,405	0/0:10,0:10:21:0,21,315	0/0:8,0:8:21:0,21,315	0/0:2,0:2:6:0,6,71	0/0:10,0:10:27:0,27,403	0/0:8,0:8:21:0,21,315	0/0:7,0:7:10:0,10,253	0/0:4,0:4:9:0,9,135	0/0:21,0:21:60:0,60,900	0/0:10,0:10:21:0,21,315	0/0:7,0:7:21:0,21,190	0/0:12,0:12:33:0,33,458	0/0:13,0:13:30:0,30,450	0/0:8,0:8:21:0,21,315	0/0:14,0:14:24:0,24,360	0/0:6,0:6:15:0,15,175	0/0:22,0:22:60:0,60,658	0/0:11,0:11:21:0,21,315	0/0:8,0:8:21:0,21,315	0/0:11,0:11:27:0,27,405	0/0:13,0:13:27:0,27,405	0/0:10,0:10:21:0,21,315	0/0:26,0:26:60:0,60,900	0/0:21,0:21:63:0,63,700	0/0:19,0:19:57:0,57,594	0/0:22,0:22:60:0,60,900	0/0:25,0:25:63:0,63,945	0/0:23,0:23:69:0,69,752	0/0:15,0:15:36:0,36,540	0/0:8,0:8:21:0,21,273	0/0:27,0:27:63:0,63,945	0/0:7,0:7:21:0,21,234	0/0:12,0:12:29:0,29,361	0/0:14,0:14:30:0,30,450	0/0:12,0:12:24:0,24,360	0/0:8,0:8:21:0,21,290	0/0:27,0:27:60:0,60,900	0/0:10,0:10:21:0,21,315	0/0:23,0:23:60:0,60,900	0/0:21,0:21:48:0,48,720	0/0:8,0:8:21:0,21,261	0/0:9,0:9:21:0,21,315	0/0:9,0:9:21:0,21,315	0/0:20,0:20:60:0,60,614	0/0:15,0:15:22:0,22,495	0/0:11,0:11:21:0,21,315	0/0:20,0:20:51:0,51,765	0/0:13,0:13:27:0,27,405	0/0:21,0:21:60:0,60,900	0/0:24,0:24:60:0,60,900	0/0:23,0:23:60:0,60,870	0/1:7,6:13:99:156,0,188	0/0:13,0:13:27:0,27,405	0/0:24,0:24:60:0,60,900	0/0:8,0:8:21:0,21,315	0/0:7,0:7:21:0,21,241	0/0:16,0:16:30:0,30,450


AN decreases because of a couple GQ0 hom-refs

ldgauthier · 2024-04-02T14:14:10Z

...tools/walkers/GenotypeGVCFs/expected/combine.single.sample.pipeline.1.include_nonvariant.vcf

-20	10030911	.	C	.	.	.	DP=1	GT:DP:RGQ	0/0:1:0
-20	10030912	.	A	.	.	.	DP=1	GT:DP:RGQ	0/0:1:0
-20	10030913	.	A	.	.	.	DP=1	GT:DP:RGQ	0/0:1:0
+20	10030900	.	T	.	.	.	DP=1	GT:DP:RGQ	./.:1:0


GQ0 hom refs with DP>0 go to no-call

ldgauthier · 2024-04-02T14:14:31Z

...tools/walkers/GenotypeGVCFs/expected/combine.single.sample.pipeline.1.include_nonvariant.vcf

-20	10031221	.	A	.	.	.	.	GT:DP:RGQ	0/0:0:0
-20	10031222	.	A	.	.	.	.	GT:DP:RGQ	0/0:0:0
-20	10031223	.	G	.	.	.	.	GT:DP:RGQ	0/0:0:0
+20	10030942	.	A	.	.	.	.	GT	./.


No data no-calls get their zero attributes stripped

ldgauthier · 2024-04-02T14:16:33Z

.../org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/expected/testSpanningDeletion.vcf

-20	10096906	.	A	*	0	LowQual	AC=2;AF=1.00;AN=2;DP=2;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;QD=-0.00;SOR=0.693	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,2:2:6:1|1:10096899_G_T:90,6,0	./.:0,0:0:0:.:.:0,0,0	./.:0,0:0:0:.:.:0,0,0
-20	10096907	.	A	.	.	.	DP=2	GT:DP:RGQ	./.:2:0	./.:0:0	./.:0:0
-20	10624924	.	TCA	T	169.53	.	AC=2;AF=0.333;AN=6;BaseQRankSum=0.103;ClippingRankSum=0.00;DP=56;ExcessHet=0.9691;FS=1.657;MLEAC=2;MLEAF=0.333;MQ=55.03;MQRankSum=0.754;QD=5.30;RAW_MQ=142331.00;ReadPosRankSum=120.50;SOR=0.287	GT:AD:DP:GQ:PGT:PID:PL	0/1:11,4:15:71:.:.:71,0,257	0/0:9,0:9:0:.:.:0,0,231	0/1:11,6:17:99:0|1:10624924_TCA_T:107,0,318
+20	10096905	.	TA	T	78.28	.	AC=2;AF=1.00;AN=2;DP=2;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=25.36;RAW_MQ=7200.00;SOR=0.693	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,2:2:6:1|1:10096899_G_T:90,6,0	./.	./.


QUAL decreases slightly once we get rid of [0,0,0] PLs

ldgauthier · 2024-04-02T14:17:24Z

...s/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/multiSamples.GATK3expected.g.vcf

-20	899938	.	G	C,*	4882.54	.	AC=19,2;AF=0.731,0.077;AN=26;AS_BaseQRankSum=-1.400,.;AS_FS=0.000,0.000;AS_InbreedingCoeff=0.5553,0.4090;AS_MQ=40.66,0.00;AS_MQRankSum=-0.700,.;AS_QD=25.00,16.50;AS_ReadPosRankSum=0.000,.;AS_SOR=1.900,0.105;BaseQRankSum=-1.383e+00;ClippingRankSum=0.00;DP=124;ExcessHet=0.0000;FS=0.000;InbreedingCoeff=0.5362;MLEAC=29,2;MLEAF=1.00,0.077;MQ=39.58;MQRankSum=-6.740e-01;QD=29.56;RAW_MQ=183275.00;ReadPosRankSum=0.00;SOR=1.811	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,3,0:3:9:1|1:899928_G_C:135,9,0,135,9,135	1/1:0,14,0:14:45:1|1:899928_G_C:675,45,0,675,45,675	1/1:0,15,0:15:43:1|1:899928_G_C:633,43,0,633,43,633	./.:0,0,0:0:0:.:.:0,0,0,0,0,0	./.:0,0,0:0:0:.:.:0,0,0,0,0,0	./.:0,0,0	./.:1,0,0:1:0:.:.:0,0,0,0,0,0	1/1:0,8,0:8:24:1|1:899928_G_C:360,24,0,360,24,360	2/2:0,0,1:1:3:1|1:899928_G_C:45,45,45,3,3,0	./.:1,0,0:1:0:.:.:0,0,0,0,0,0	./.:2,0,0:2:0:.:.:0,0,0,0,0,0	./.:1,0,0:1:0:.:.:0,0,0,0,0,0	1/1:0,6,0:6:18:1|1:899928_G_C:270,18,0,270,18,270	./.:0,0,0	0/1:2,2,0:4:78:0|1:899928_G_C:78,0,282,84,288,372	./.:0,0,0:0:0:.:.:0,0,0,0,0,0	1/1:0,48,0:48:99:1|1:899928_G_C:2194,147,0,2194,147,2194	1/1:0,4,0:4:12:1|1:899928_G_C:180,12,0,180,12,180	./.:2,0,0:2:0:.:.:0,0,0,0,0,0	0/0:6,0,0:6:15:.:.:0,15,225,15,225,225	1/1:0,4,0:4:12:1|1:899928_G_C:180,12,0,180,12,180	1/1:0,2,0:2:6:1|1:899928_G_C:90,6,0,90,6,90	./.:0,0,0:0:0:.:.:0,0,0,0,0,0	0/0:1,0,0:1:3:.:.:0,3,36,3,36,36
-20	899942	.	G	A	4913.79	.	AC=19;AF=0.792;AN=24;AS_BaseQRankSum=0.400;AS_FS=0.000;AS_InbreedingCoeff=0.5567;AS_MQ=44.39;AS_MQRankSum=-0.300;AS_QD=30.62;AS_ReadPosRankSum=-1.500;AS_SOR=1.893;BaseQRankSum=0.493;ClippingRankSum=0.00;DP=148;ExcessHet=0.0000;FS=0.000;InbreedingCoeff=0.4850;MLEAC=30;MLEAF=1.00;MQ=43.13;MQRankSum=-2.530e-01;QD=28.17;RAW_MQ=264157.00;ReadPosRankSum=-1.501e+00;SOR=1.923	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,3:3:9:1|1:899928_G_C:135,9,0	1/1:0,15:15:45:1|1:899928_G_C:636,45,0	1/1:0,16:16:45:1|1:899928_G_C:636,45,0	./.:0,0:0:0:.:.:0,0,0	./.:0,0:0:0:.:.:0,0,0	./.:0,0	./.:1,0:1:0:.:.:0,0,0	1/1:0,9:9:27:1|1:899928_G_C:366,27,0	./.:3,0:3:0:.:.:0,0,0	./.:0,0:0:0:.:.:0,0,0	./.:2,0:2:0:.:.:0,0,0	./.:1,0:1:0:.:.:0,0,0	1/1:0,7:7:19:1|1:899928_G_C:273,19,0	./.:0,0	0/1:2,8:10:88:0|1:899928_G_C:88,0,274	./.:0,0:0:0:.:.:0,0,0	1/1:0,58:58:99:1|1:899928_G_C:2217,159,0	1/1:0,5:5:13:1|1:899928_G_C:183,13,0	./.:2,0:2:0:.:.:0,0,0	0/0:5,0:5:15:.:.:0,15,178	1/1:0,7:7:16:1|1:899928_G_C:189,16,0	1/1:0,2:2:6:1|1:899928_G_C:90,6,0	./.:0,0:0:0:.:.:0,0,0	0/0:1,0:1:3:.:.:0,3,36
+20	899928	.	G	C	4944.58	.	AC=21;AF=0.808;AN=26;AS_BaseQRankSum=-1.400;AS_FS=0.000;AS_InbreedingCoeff=0.5339;AS_MQ=43.54;AS_MQRankSum=-0.700;AS_QD=25.36;AS_ReadPosRankSum=0.000;AS_SOR=1.863;BaseQRankSum=-1.383e+00;ClippingRankSum=0.00;DP=133;ExcessHet=0.0000;FS=0.000;InbreedingCoeff=0.5089;MLEAC=25;MLEAF=0.962;MQ=42.34;MQRankSum=-6.740e-01;QD=28.73;RAW_MQ=222270.00;ReadPosRankSum=0.00;SOR=1.781	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,3:3:9:1|1:899928_G_C:135,9,0	1/1:0,18:18:54:1|1:899928_G_C:767,54,0	1/1:0,15:15:45:1|1:899928_G_C:640,45,0	./.	./.	./.	./.	1/1:0,9:9:27:1|1:899928_G_C:370,27,0	1/1:0,1:1:3:1|1:899928_G_C:45,3,0	./.:1,0:1:0:.:.:0,0,0	./.:2,0:2:0:.:.:0,0,0	./.:3,0:3:0:.:.:0,0,0	1/1:0,5:5:15:1|1:899928_G_C:225,15,0	./.	0/1:2,2:4:78:0|1:899928_G_C:78,0,282	./.	1/1:0,51:51:99:1|1:899928_G_C:2229,153,0	1/1:0,3:3:9:1|1:899928_G_C:135,9,0	./.:2,0:2:0:.:.:0,0,0	0/0:7,0:7:21:.:.:0,21,236	1/1:0,4:4:12:1|1:899928_G_C:168,12,0	1/1:0,2:2:6:1|1:899928_G_C:90,6,0	./.	0/0:2,0:2:6:.:.:0,6,65
+20	899933	.	GGGGGGCGC	G	30.86	.	AC=2;AF=0.063;AN=32;AS_BaseQRankSum=.;AS_FS=0.000;AS_InbreedingCoeff=0.2616;AS_MQ=60.00;AS_MQRankSum=.;AS_QD=30.97;AS_ReadPosRankSum=.;AS_SOR=0.693;DP=128;ExcessHet=0.0000;FS=0.000;InbreedingCoeff=0.3190;MLEAC=1;MLEAF=0.031;MQ=34.64;QD=30.86;RAW_MQ=3600.00;SOR=1.609	GT:AD:DP:GQ:PGT:PID:PL	0/0:3,0:3:9:.:.:0,9,97	0/0:18,0:18:27:.:.:0,27,405	0/0:15,0:15:24:.:.:0,24,360	./.	./.	./.	./.	0/0:8,0:8:21:.:.:0,21,315	1/1:0,1:1:3:1|1:899928_G_C:45,3,0	0/0:1,0:1:3:.:.:0,3,33	./.:2,0:2:0:.:.:0,0,0	0/0:1,0:1:3:.:.:0,3,34	0/0:6,0:6:15:.:.:0,15,225	./.	0/0:4,0:4:9:.:.:0,9,135	./.	0/0:52,0:52:99:.:.:0,120,1800	0/0:3,0:3:9:.:.:0,9,115	0/0:2,0:2:3:.:.:0,3,45	0/0:6,0:6:15:.:.:0,15,225	0/0:3,0:3:6:.:.:0,6,90	0/0:2,0:2:6:.:.:0,6,77	./.	0/0:1,0:1:3:.:.:0,3,36


Annotations like InbreedingCoeff (and sometimes ExcessHet) may also change once we get rid of 0,0,0 PLs

ldgauthier · 2024-04-02T14:18:22Z

src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/noReads.g.vcf

+##reference=file:///humgen/1kg/reference/human_g1k_v37_decoy.fasta
+##source=CombineGVCFs
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	FAKE_SAMPLE	GTEX-RVPV-0003
+20	10000000	.	T	G,<NON_REF>	.	.	DP=2;ExcessHet=3.01;RAW_MQ=7200.00	GT:AD:DP:GQ:MIN_DP:PL:SB	./.:0,2,0:2:6:.:49,6,0,49,6,49:0,0,1,1	./.:.:0:0:0:0,0,0,0,0,0


Input GVCF here has the "no data" no-call with zeros, but this will get cleaned up by GGVCFs

ldgauthier · 2024-04-02T14:22:35Z

...roadinstitute/hellbender/tools/walkers/GenotypeGVCFs/multiallelicQualRegression.expected.vcf

-chr1	62121342	.	T	TAAA,TA,TTAAA,TTAA,TAA,TTA	22320.99	.	AC=15,55,5,2,7,1;AF=0.117,0.430,0.039,0.016,0.055,7.813e-03;AN=128;BaseQRankSum=-1.710e-01;DP=2025;ExcessHet=7.3807;FS=0.000;InbreedingCoeff=-0.1398;MLEAC=15,55,5,2,7,1;MLEAF=0.117,0.430,0.039,0.016,0.055,7.813e-03;MQ=59.87;MQRankSum=0.00;QD=21.69;ReadPosRankSum=-2.820e-01;SOR=1.746	GT:AD:DP:GQ:PL	0/1:3,7,0,0,0,0,0:10:54:225,0,54,233,78,311,233,78,311,311,233,78,311,311,311,233,78,311,311,311,311,233,78,311,311,311,311,311	0/2:6,0,5,0,0,0,0:13:94:94,125,289,0,149,140,125,289,149,289,125,289,149,289,289,125,289,149,289,289,289,125,289,149,289,289,289,289	0/2:4,0,4,0,0,0,0:8:82:82,94,188,0,94,82,94,188,94,188,94,188,94,188,188,94,188,94,188,188,188,94,188,94,188,188,188,188	0/2:5,0,6,0,0,0,0:11:80:118,132,231,0,98,80,132,231,98,231,132,231,98,231,231,132,231,98,231,231,231,132,231,98,231,231,231,231	.:0,0,0,0,0,0,0	2/3:0,0,2,3,0,0,0:10:70:653,606,694,546,531,525,70,192,0,219,606,694,531,192,694,606,694,531,192,694,694,606,694,531,192,694,694,694	0/0:30,0,0,0,0,0,0:30:60	0/2:14,0,7,0,0,0,0:21:99:122,164,477,0,313,292,164,477,313,477,164,477,313,477,477,164,477,313,477,477,477,164,477,313,477,477,477,477	1/2:2,9,17,0,0,0,0:32:99:808,399,550,303,0,259,701,456,315,725,701,456,315,725,725,701,456,315,725,725,725,701,456,315,725,725,725,725	2/2:2,0,19,0,0,0,0:21:12:437,443,487,12,57,0,443,487,57,487,443,487,57,487,487,443,487,57,487,487,487,443,487,57,487,487,487,487	0/1:21,7,0,0,0,0,0:28:99:176,0,806,240,826,1066,240,826,1066,1066,240,826,1066,1066,1066,240,826,1066,1066,1066,1066,240,826,1066,1066,1066,1066,1066	0/4:14,0,0,0,15,0,0:31:99:454,507,1094,507,1094,1094,507,1094,1094,1094,0,642,642,642,793,507,1094,1094,1094,642,1094,507,1094,1094,1094,642,1094,1094	1/2:1,8,12,0,0,0,0:25:99:761,272,383,369,0,335,753,420,404,872,753,420,404,872,872,753,420,404,872,872,872,753,420,404,872,872,872,872	2/2:1,0,14,0,0,0,0:15:17:294,297,321,17,41,0,297,321,41,321,297,321,41,321,321,297,321,41,321,321,321,297,321,41,321,321,321,321	0/2:15,0,10,0,0,0,0:25:99:185,230,583,0,353,323,230,583,353,583,230,583,353,583,583,230,583,353,583,583,583,230,583,353,583,583,583,583	0/2:4,0,13,0,0,0,0:17:40:259,271,349,0,78,40,271,349,78,349,271,349,78,349,349,271,349,78,349,349,349,271,349,78,349,349,349,349	3/4:0,0,0,17,6,0,0:23:87:1500,1113,1005,1113,1005,1005,206,202,202,87,472,464,464,0,353,1113,1005,1005,202,464,1005,1113,1005,1005,202,464,1005,1005	1/2:2,4,6,0,0,0,0:15:99:344,110,215,142,0,148,283,176,171,327,283,176,171,327,327,283,176,171,327,327,327,283,176,171,327,327,327,327	0/2:8,0,7,0,0,0,0:16:99:138,158,372,0,186,147,158,372,186,372,158,372,186,372,372,158,372,186,372,372,372,158,372,186,372,372,372,372	0/2:3,0,18,0,0,0,0:21:16:413,422,492,0,70,16,422,492,70,492,422,492,70,492,492,422,492,70,492,492,492,422,492,70,492,492,492,492	1/2:1,7,12,0,0,0,0:20:99:589,302,383,243,0,191,584,367,247,619,584,367,247,619,619,584,367,247,619,619,619,584,367,247,619,619,619,619	1/2:2,2,9,0,0,0,0:17:99:418,195,316,115,0,111,332,303,133,411,332,303,133,411,411,332,303,133,411,411,411,332,303,133,411,411,411,411	1/5:0,10,0,0,0,3,0:13:36:605,82,36,489,81,450,489,81,450,450,489,81,450,450,450,262,0,259,259,259,215,489,81,450,450,450,259,450	0/2:5,0,22,0,0,0,0:27:36:502,517,619,0,102,36,517,619,102,619,517,619,102,619,619,517,619,102,619,619,619,517,619,102,619,619,619,619	0/2:5,0,28,0,0,0,0:33:17:661,675,777,0,101,17,675,777,101,777,675,777,101,777,777,675,777,101,777,777,777,675,777,101,777,777,777,777	0/3:8,0,0,5,0,0,0:17:99:428,473,1081,473,1081,1081,0,629,629,643,473,1081,1081,629,1081,473,1081,1081,629,1081,1081,473,1081,1081,629,1081,1081,1081	0/2:10,0,9,0,0,0,0:19:99:181,211,448,0,237,210,211,448,237,448,211,448,237,448,448,211,448,237,448,448,448,211,448,237,448,448,448,448	0/2:5,0,13,0,0,0,0:20:71:327,325,461,0,125,71,325,461,125,461,325,461,125,461,461,325,461,125,461,461,461,325,461,125,461,461,461,461	1/2:0,4,8,0,0,0,0:14:99:496,217,245,203,0,157,412,266,182,448,412,266,182,448,448,412,266,182,448,448,448,412,266,182,448,448,448,448	1/5:0,10,0,0,0,6,0:16:99:665,159,108,546,155,504,546,155,504,504,546,155,504,504,504,239,0,236,236,236,186,546,155,504,504,504,236,504	0/2:8,0,5,0,0,0,0:13:89:89,113,286,0,172,157,113,286,172,286,113,286,172,286,286,113,286,172,286,286,286,113,286,172,286,286,286,286	2/5:1,0,7,0,0,4,0:16:95:336,282,291,114,120,95,282,291,120,291,282,291,120,291,291,139,168,0,168,168,145,282,291,120,291,291,168,291	0/2:5,0,13,0,0,0,0:18:81:290,305,425,0,120,81,305,425,120,425,305,425,120,425,425,305,425,120,425,425,425,305,425,120,425,425,425,425	1/2:3,6,4,0,0,0,0:16:49:218,54,1171,49,0,82,175,162,110,258,175,162,110,258,258,175,162,110,258,258,258,175,162,110,258,258,258,258	2/5:1,0,11,0,0,3,0:17:44:388,331,349,70,82,44,331,349,82,349,331,349,82,349,349,234,264,0,264,264,248,331,349,82,349,349,264,349	2/2:2,0,19,0,0,0,0:21:9:427,433,481,9,57,0,433,481,57,481,433,481,57,481,481,433,481,57,481,481,481,433,481,57,481,481,481,481	0/2:11,0,9,0,0,0,0:20:99:178,211,470,0,259,232,211,470,259,470,211,470,259,470,470,211,470,259,470,470,470,211,470,259,470,470,470,470	0/2:4,0,25,0,0,0,0:29:0:596,608,686,0,78,0,608,686,78,686,608,686,78,686,686,608,686,78,686,686,686,608,686,78,686,686,686,686	1/2:2,4,3,0,0,0,0:9:30:280,30,114,140,0,157,259,113,187,319,259,113,187,319,319,259,113,187,319,319,319,259,113,187,319,319,319,319	0/0:28,0,0,0,0,0,0:28:30	0/2:5,0,28,0,0,0,0:33:10:645,658,752,0,94,10,658,752,94,752,658,752,94,752,752,658,752,94,752,752,752,658,752,94,752,752,752,752	0/2:12,0,10,0,0,0,0:22:99:198,234,501,0,267,237,234,501,267,501,234,501,267,501,501,234,501,267,501,501,501,234,501,267,501,501,501,501	1/2:0,4,12,0,0,0,0:22:99:559,320,367,209,0,150,489,361,164,497,489,361,164,497,497,489,361,164,497,497,497,489,361,164,497,497,497,497	0/2:9,0,10,0,0,0,0:19:99:191,218,430,0,212,182,218,430,212,430,218,430,212,430,430,218,430,212,430,430,430,218,430,212,430,430,430,430	2/5:1,0,12,0,0,4,0:17:53:382,372,394,74,99,53,372,394,99,394,372,394,99,394,394,251,283,0,283,283,273,372,394,99,394,394,283,394	2/2:0,0,13,0,0,0,0:13:39:343,343,344,39,39,0,343,344,39,344,343,344,39,344,344,343,344,39,344,344,344,343,344,39,344,344,344,344	0/2:2,0,15,0,0,0,0:17:0:352,358,405,0,48,0,358,405,48,405,358,405,48,405,405,358,405,48,405,405,405,358,405,48,405,405,405,405	0/2:6,0,15,0,0,0,0:21:92:368,387,527,0,140,92,387,527,140,527,387,527,140,527,527,387,527,140,527,527,527,387,527,140,527,527,527,527	0/2:3,0,18,0,0,0,0:21:17:396,405,476,0,71,17,405,476,71,476,405,476,71,476,476,405,476,71,476,476,476,405,476,71,476,476,476,476	0/2:3,0,18,0,0,0,0:21:14:432,441,512,0,71,14,441,512,71,512,441,512,71,512,512,441,512,71,512,512,512,441,512,71,512,512,512,512	0/2:2,0,5,0,0,0,0:12:50:119,133,203,0,70,50,133,203,70,203,133,203,70,203,203,133,203,70,203,203,203,133,203,70,203,203,203,203	0/5:8,0,0,0,0,4,0:12:92:92,117,386,117,386,386,117,386,386,386,117,386,386,386,386,0,269,269,269,269,257,117,386,386,386,386,269,386	3/6:0,0,0,13,0,0,4:17:94:1317,1011,924,1011,924,924,200,195,195,94,1011,924,924,195,924,1011,924,924,195,924,924,489,478,478,0,478,478,386	0/3:29,0,0,5,0,0,0:38:99:447,352,1473,352,1473,1473,0,1179,1179,1147,352,1473,1473,1179,1473,352,1473,1473,1179,1473,1473,352,1473,1473,1179,1473,1473,1473	0/0:33,0,0,0,0,0,0:33:10	1/2:2,4,7,0,0,0,0:16:99:351,132,245,139,0,151,322,266,179,445,322,266,179,445,445,322,266,179,445,445,445,322,266,179,445,445,445,445	2/2:1,0,16,0,0,0,0:19:29:416,412,436,29,54,0,412,436,54,436,412,436,54,436,436,412,436,54,436,436,436,412,436,54,436,436,436,436	0/1:11,5,0,0,0,0,0:16:99:198,0,407,231,428,659,231,428,659,659,231,428,659,659,659,231,428,659,659,659,659,231,428,659,659,659,659,659	0/0:32,0,0,0,0,0,0:32:40	2/2:2,0,16,0,0,0,0:18:1:369,375,422,1,48,0,375,422,48,422,375,422,48,422,422,375,422,48,422,422,422,375,422,48,422,422,422,422	2/5:0,0,7,0,0,3,0:10:55:280,267,260,86,83,55,267,260,83,260,267,260,83,260,260,163,163,0,163,163,151,267,260,83,260,260,163,260	0/0:14,0,0,0,0,0,0:14:10	2/2:0,0,3,0,0,0,0:3:9:79,79,79,9,9,0,79,79,9,79,79,79,9,79,79,79,79,9,79,79,79,79,79,9,79,79,79,79	0/2:5,0,3,0,0,0,0:8:39:39,54,171,0,117,108,54,171,117,171,54,171,117,171,171,54,171,117,171,171,171,54,171,117,171,171,171,171	0/2:15,0,4,0,0,0,0:19:71:71,117,471,0,354,339,117,471,354,471,117,471,354,471,471,117,471,354,471,471,471,117,471,354,471,471,471,471
-chr1	62578717	.	CAAAA	CAAAAA,C,CAA,CAAAAAA,CAAA,CAAAAAAAA	1557.32	.	AC=14,2,2,8,7,1;AF=0.179,0.026,0.026,0.103,0.090,0.013;AN=78;BaseQRankSum=0.00;DP=580;ExcessHet=0.4134;FS=0.000;InbreedingCoeff=0.1666;MLEAC=14,2,2,8,8,1;MLEAF=0.179,0.026,0.026,0.103,0.103,0.013;MQ=50.49;MQRankSum=-2.530e-01;QD=10.59;ReadPosRankSum=0.566;SOR=1.522	GT:AD:DP:GQ:PL	0/0:0,0,0,0,0,0,0:1:0:0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0	.:0,0,0,0,0,0,0	.:0,0,0,0,0,0,0	.:0,0,0,0,0,0,0	.:0,0,0,0,0,0,0	0/0:27,0,0,0,0,0,0:27:10	0/1:2,4,0,0,0,0,0:6:13:52,0,13,58,24,82,58,24,82,82,58,24,82,82,82,58,24,82,82,82,82,58,24,82,82,82,82,82	0/2:5,0,4,0,0,0,0:9:99:122,141,311,0,171,158,141,311,171,311,141,311,171,311,311,141,311,171,311,311,311,141,311,171,311,311,311,311	.:0,0,0,0,0,0,0	.:0,0,0,0,0,0,0	0/0:11,0,0,0,0,0,0:11:10	.:0,0,0,0,0,0,0	1/3:0,4,0,5,0,0,0:9:76:152,100,125,188,136,277,76,0,172,228,188,136,277,172,277,188,136,277,172,277,277,188,136,277,172,277,277,277	0/0:12,0,0,0,0,0,0:12:30	0/4:2,0,0,0,3,0,0:5:25:63,70,103,70,103,103,70,103,103,103,0,34,34,34,25,70,103,103,103,34,103,70,103,103,103,34,103,103	0/1:2,5,0,0,0,0,0:7:10:70,0,10,76,25,101,76,25,101,101,76,25,101,101,101,76,25,101,101,101,101,76,25,101,101,101,101,101	0/1:5,3,0,0,0,0,0:8:34:34,0,65,48,74,122,48,74,122,122,48,74,122,122,122,48,74,122,122,122,122,48,74,122,122,122,122,122	.:0,0,0,0,0,0,0	0/0:18,0,0,0,0,0,0:18:10	1/1:0,3,0,0,0,0,0:3:10:61,10,0,61,10,61,61,10,61,61,61,10,61,61,61,61,10,61,61,61,61,61,10,61,61,61,61,61	1/5:1,2,0,0,0,4,0:7:21:69,49,89,85,85,129,85,85,129,129,85,85,129,129,129,21,0,57,57,57,58,85,85,129,129,129,57,129	0/1:1,2,0,0,0,0,0:3:1:31,0,1,33,7,41,33,7,41,41,33,7,41,41,41,33,7,41,41,41,41,33,7,41,41,41,41,41	0/0:17,0,0,0,0,0,0:17:10	1/1:0,6,0,0,0,0,0:6:18:120,18,0,120,19,122,120,19,122,122,120,19,122,122,122,120,19,122,122,122,122,120,19,122,122,122,122,122	0/4:2,0,0,0,2,0,0:4:46:49,55,108,55,108,108,55,108,108,108,0,54,54,54,46,55,108,108,108,54,108,55,108,108,108,54,108,108	0/0:17,0,0,0,0,0,0:17:10	0/4:2,0,0,0,2,0,0:4:46:48,54,108,54,108,108,54,108,108,108,0,54,54,54,46,54,108,108,108,54,108,54,108,108,108,54,108,108	.:0,0,0,0,0,0,0	0/5:5,0,0,0,0,2,0:10:41:41,59,197,59,197,197,59,197,197,197,59,197,197,197,197,0,87,87,87,87,54,59,197,197,197,197,87,197	1/5:1,2,0,0,0,2,0:5:21:47,22,48,57,48,87,57,48,87,87,57,48,87,87,87,21,0,47,47,47,47,57,48,87,87,87,47,87	0/0:18,0,0,0,0,0,0:18:10	1/5:0,2,0,0,0,3,0:5:39:82,56,72,94,71,117,94,71,117,117,94,71,117,117,117,39,0,57,57,57,61,94,71,117,117,117,57,117	.:0,0,0,0,0,0,0	.:0,0,0,0,0,0,0	.:0,0,0,0,0,0,0	.:0,0,0,0,0,0,0	0/0:8,0,0,0,0,0,0:8:20	.:0,0,0,0,0,0,0	0/4:4,0,0,0,4,0,0:8:64:64,76,160,76,160,160,76,160,160,160,0,84,84,84,72,76,160,160,160,84,160,76,160,160,160,84,160,160	0/3:2,0,0,2,0,0,0:4:47:49,55,108,55,108,108,0,54,54,47,55,108,108,54,108,55,108,108,54,108,108,55,108,108,54,108,108,108	.:0,0,0,0,0,0,0	.:0,0,0,0,0,0,0	0/5:1,0,0,0,0,2,0:3:2:22,24,32,24,32,32,24,32,32,32,24,32,32,32,32,0,7,7,7,7,2,24,32,32,32,32,7,32	0/0:19,0,0,0,0,0,0:19:20	0/1:3,3,0,0,0,0,0:6:30:41,0,30,50,39,89,50,39,89,89,50,39,89,89,89,50,39,89,89,89,89,50,39,89,89,89,89,89	.:0,0,0,0,0,0,0	0/0:15,0,0,0,0,0,0:15:20	0/0:18,0,0,0,0,0,0:18:10	4/5:0,0,0,0,2,3,0:7:57:113,130,194,130,194,194,130,194,194,194,73,114,114,114,125,57,88,88,88,0,74,130,194,194,194,114,88,194	0/0:2,0,0,0,0,0,0:7:19:0,19,105,19,105,105,19,105,105,105,19,105,105,105,105,19,105,105,105,105,105,19,105,105,105,105,105,105	.:0,0,0,0,0,0,0	0/2:6,0,2,0,0,0,0:8:54:54,72,313,0,241,235,72,313,241,313,72,313,241,313,313,72,313,241,313,313,313,72,313,241,313,313,313,313	0/5:5,0,0,0,0,3,0:8:28:28,42,106,42,106,106,42,106,106,106,42,106,106,106,106,0,64,64,64,64,56,42,106,106,106,106,64,106	0/4:3,0,0,0,5,0,0:8:55:112,121,192,121,192,192,121,192,192,192,0,71,71,71,55,121,192,192,192,71,192,121,192,192,192,71,192,192	.:0,0,0,0,0,0,0	1/6:1,2,0,0,0,0,4:7:33:174,97,85,163,103,182,163,103,182,182,163,103,182,182,182,163,103,182,182,182,182,33,0,69,69,69,69,74	.:0,0,0,0,0,0,0	.:0,0,0,0,0,0,0	4/4:0,0,0,0,2,0,0:2:6:49,49,49,49,49,49,49,49,49,49,6,6,6,6,0,49,49,49,49,6,49,49,49,49,49,6,49,49	.:0,0,0,0,0,0,0	0/0:10,0,0,0,0,0,0:10:10	.:0,0,0,0,0,0,0	.:0,0,0,0,0,0,0	.:0,0,0,0,0,0,0	.:0,0,0,0,0,0,0
-chr1	64634018	.	GT	GTT,G,GTTT,GTTTTTT,GTTTT	6096.03	.	AC=20,15,3,1,1;AF=0.169,0.127,0.025,8.475e-03,8.475e-03;AN=118;BaseQRankSum=0.00;DP=2091;ExcessHet=32.0677;FS=1.168;InbreedingCoeff=-0.4330;MLEAC=20,16,3,1,1;MLEAF=0.169,0.136,0.025,8.475e-03,8.475e-03;MQ=59.14;MQRankSum=0.00;QD=6.38;ReadPosRankSum=-1.460e-01;SOR=0.862	GT:AD:DP:GQ:PGT:PID:PL	0/1:7,15,0,0,0,0:24:99:.:.:311,0,141,363,182,591,363,182,591,591,363,182,591,591,591,363,182,591,591,591,591	1/2:2,6,2,0,0,0:11:23:.:.:187,23,137,130,0,191,202,94,206,304,202,94,206,304,304,202,94,206,304,304,304	0/2:10,0,3,0,0,0:13:23:0|1:64634018_GT_G:23,52,280,0,228,219,52,280,228,280,52,280,228,280,280,52,280,228,280,280,280	0/0:6,0,0,0,0,0:14:17:.:.:0,17,214,17,214,214,17,214,214,214,17,214,214,214,214,17,214,214,214,214,214	.:0,0,0,0,0,0	0/1:23,9,0,0,0,0:35:97:.:.:97,0,454,162,504,717,162,504,717,717,162,504,717,717,717,162,504,717,717,717,717	0/0:30,0,0,0,0,0:30:60	./.:15,0,0,0,0,0:15:0	0/2:25,0,7,0,0,0:34:99:.:.:102,191,848,0,514,420,191,848,514,848,191,848,514,848,848,191,848,514,848,848,848	0/0:28,0,0,0,0,0:28:60	0/1:11,15,0,0,0,0:26:99:0|1:64634018_G_GT:300,0,166,332,209,540,332,209,540,540,332,209,540,540,540,332,209,540,540,540,540	0/0:34,0,0,0,0,0:34:20	0/0:32,0,0,0,0,0:32:60	0/0:43,0,0,0,0,0:43:30	0/1:7,22,0,0,0,0:34:76:.:.:499,0,76,575,146,828,575,146,828,828,575,146,828,828,828,575,146,828,828,828,828	0/1:9,17,0,0,0,0:26:99:0|1:64634018_G_GT:325,0,128,352,174,526,352,174,526,526,352,174,526,526,526,352,174,526,526,526,526	0/1:15,7,0,0,0,0:22:79:.:.:79,0,281,124,302,426,124,302,426,426,124,302,426,426,426,124,302,426,426,426,426	0/1:17,6,0,0,0,0:25:24:.:.:24,0,375,92,403,575,92,403,575,575,92,403,575,575,575,92,403,575,575,575,575	0/3:8,0,0,11,0,0:35:99:.:.:264,334,632,334,632,632,0,288,288,449,334,632,632,288,632,334,632,632,288,632,632	0/1:12,23,0,0,0,0:42:99:.:.:567,0,226,638,286,976,638,286,976,976,638,286,976,976,976,638,286,976,976,976,976	0/0:24,0,0,0,0,0:24:30	0/1:17,7,0,0,0,0:28:90:.:.:90,0,444,154,458,613,154,458,613,613,154,458,613,613,613,154,458,613,613,613,613	0/0:33,0,0,0,0,0:33:50	0/3:14,0,0,14,0,0:30:99:.:.:274,342,851,342,851,851,0,486,486,579,342,851,851,486,851,342,851,851,486,851,851	0/0:39,0,0,0,0,0:39:60	0/0:26,0,0,0,0,0:39:99:.:.:0,105,1113,105,1113,1113,105,1113,1113,1113,105,1113,1113,1113,1113,105,1113,1113,1113,1113,1113	0/0:33,0,0,0,0,0:33:10	0/4:12,0,0,0,10,0:27:99:.:.:280,354,891,354,891,891,354,891,891,891,0,518,518,518,674,354,891,891,891,518,891	0/2:31,0,10,0,0,0:43:97:.:.:97,221,1092,0,855,881,221,1092,855,1092,221,1092,855,1092,1092,221,1092,855,1092,1092,1092	.:0,0,0,0,0,0	0/2:28,0,5,0,0,0:36:23:.:.:23,108,979,0,768,701,108,979,768,979,108,979,768,979,979,108,979,768,979,979,979	0/2:18,0,10,0,0,0:36:99:.:.:143,232,1037,0,788,750,232,1037,788,1037,232,1037,788,1037,1037,232,1037,788,1037,1037,1037	0/1:16,8,0,0,0,0:24:68:.:.:68,0,260,114,280,394,114,280,394,394,114,280,394,394,394,114,280,394,394,394,394	0/0:41,0,0,0,0,0:41:50	0/2:14,0,3,0,0,0:17:31:.:.:31,70,312,0,242,233,70,312,242,312,70,312,242,312,312,70,312,242,312,312,312	0/2:15,0,3,0,0,0:18:21:.:.:21,65,343,0,278,269,65,343,278,343,65,343,278,343,343,65,343,278,343,343,343	0/2:23,0,5,0,0,0:29:40:.:.:40,123,787,0,670,698,123,787,670,787,123,787,670,787,787,123,787,670,787,787,787	0/0:37,0,0,0,0,0:37:40	0/1:17,5,0,0,0,0:22:65:.:.:65,0,303,115,320,436,115,320,436,436,115,320,436,436,436,115,320,436,436,436,436	0/0:25,0,0,0,0,0:25:60	0/0:34,0,0,0,0,0:34:20	0/1:18,10,0,0,0,0:28:99:0|1:64634018_G_GT:216,0,248,267,279,546,267,279,546,546,267,279,546,546,546,267,279,546,546,546,546	0/2:27,0,6,0,0,0:37:24:.:.:24,130,917,0,790,843,130,917,790,917,130,917,790,917,917,130,917,790,917,917,917	./.:38,0,0,0,0,0:38:0	0/0:30,0,0,0,0,0:30:60	0/2:15,0,5,0,0,0:20:70:.:.:70,115,556,0,441,426,115,556,441,556,115,556,441,556,556,115,556,441,556,556,556	0/5:10,0,0,0,0,18:32:99:.:.:501,561,1230,561,1230,1230,561,1230,1230,1230,561,1230,1230,1230,1230,0,626,626,626,626,608	0/2:13,0,4,0,0,0:24:31:.:.:31,106,844,0,664,619,106,844,664,844,106,844,664,844,844,106,844,664,844,844,844	0/0:28,0,0,0,0,0:33:84:0|1:64634018_GTT_G:0,84,1005,84,1005,1005,84,1005,1005,1005,84,1005,1005,1005,1005,84,1005,1005,1005,1005,1005	0/1:9,17,0,0,0,0:26:98:0|1:64634018_G_GT:395,0,98,421,148,569,421,148,569,569,421,148,569,569,569,421,148,569,569,569,569	0/2:15,0,6,0,0,0:23:62:.:.:62,132,599,0,469,526,132,599,469,599,132,599,469,599,599,132,599,469,599,599,599	0/1:9,12,0,0,0,0:26:99:.:.:313,0,119,287,185,477,287,185,477,477,287,185,477,477,477,287,185,477,477,477,477	0/1:7,13,0,0,0,0:24:99:.:.:220,0,114,280,157,503,280,157,503,503,280,157,503,503,503,280,157,503,503,503,503	0/0:33,0,0,0,0,0:33:10	0/2:29,0,5,0,0,0:34:18:.:.:18,102,684,0,581,567,102,684,581,684,102,684,581,684,684,102,684,581,684,684,684	0/3:8,0,0,13,0,0:35:99:.:.:450,491,710,491,710,710,0,211,211,208,491,710,710,211,710,491,710,710,211,710,710	0/1:25,5,0,0,0,0:32:2:.:.:2,0,737,110,759,1029,110,759,1029,1029,110,759,1029,1029,1029,110,759,1029,1029,1029,1029	0/2:35,0,6,0,0,0:41:21:0|1:64634018_GT_G:21,125,1079,0,954,936,125,1079,954,1079,125,1079,954,1079,1079,125,1079,954,1079,1079,1079	0/0:17,0,0,0,0,0:20:48:.:.:0,48,467,48,467,467,48,467,467,467,48,467,467,467,467,48,467,467,467,467,467	0/1:13,4,0,0,0,0:17:22:0|1:64634018_G_GT:22,0,290,60,302,361,60,302,361,361,60,302,361,361,361,60,302,361,361,361,361	0/1:19,5,0,0,0,0:24:32:.:.:32,0,467,89,483,573,89,483,573,573,89,483,573,573,573,89,483,573,573,573,573	.:0,0,0,0,0,0	0/1:2,0,0,0,0,0:9:0:.:.:27,0,69,0,69,69,0,69,69,69,0,69,69,69,69,0,69,69,69,69,69	./.:5,0,0,0,0,0:5:0	0/0:28,0,0,0,0,0:28:30
+chr1	3836468	.	GTTTT	GTTTTT,GTTTTTTT,G,GTTTTTT	881.67	.	AC=3,2,1,3;AF=0.026,0.018,8.772e-03,0.026;AN=114;BaseQRankSum=0.00;DP=2100;ExcessHet=0.1247;FS=2.272;InbreedingCoeff=0.1698;MLEAC=2,2,1,3;MLEAF=0.018,0.018,8.772e-03,0.026;MQ=54.73;MQRankSum=0.00;QD=10.37;ReadPosRankSum=-2.300e-01;SOR=0.483	GT:AD:DP:GQ:PL	0/1:11,22,0,0,0:44:99:239,0,174,338,219,636,338,219,636,636,338,219,636,636,636	0/0:27,0,0,0,0:27:50	0/0:30,0,0,0,0:30:10	0/0:28,0,0,0,0:28:10	./.:3,0,0,0,0:3:0	0/0:27,0,0,0,0:27:60	0/0:59,0,0,0,0:59:30	0/2:3,0,7,0,0:10:59:132,142,223,0,80,59,142,223,80,223,142,223,80,223,223	0/0:33,0,0,0,0:33:60	0/0:31,0,0,0,0:31:60	.	0/0:27,0,0,0,0:27:60	0/0:30,0,0,0,0:30:60	0/0:51,0,0,0,0:51:40	0/0:29,0,0,0,0:29:60	0/0:31,0,0,0,0:31:60	0/3:8,0,0,4,0:14:99:103,160,534,160,534,534,0,437,437,670,160,534,534,437,534	0/0:30,0,0,0,0:30:60	0/0:32,0,0,0,0:32:60	0/0:37,0,0,0,0:37:60	0/0:49,0,0,0,0:49:40	0/0:36,0,0,0,0:36:60	0/2:2,0,2,0,0:4:34:34,42,113,0,71,65,42,113,71,113,42,113,71,113,113	0/0:10,0,0,0,0:14:29:0,29,176,29,176,176,29,176,176,176,29,176,176,176,176	0/0:58,0,0,0,0:58:30	0/0:32,0,0,0,0:32:60	0/0:11,0,0,0,0:13:34:0,34,285,34,285,285,34,285,285,285,34,285,285,285,285	0/0:26,0,0,0,0:26:60	0/0:26,0,0,0,0:26:60	0/0:32,0,0,0,0:32:60	.	0/0:29,0,0,0,0:29:60	0/4:1,0,0,0,6:11:35:94,175,487,175,487,487,175,487,487,487,0,90,90,90,35	0/0:40,0,0,0,0:40:10	0/0:41,0,0,0,0:41:60	0/0:30,0,0,0,0:30:60	0/4:2,0,0,0,9:11:10:186,193,234,193,234,234,193,234,234,234,0,41,41,41,10	0/0:43,0,0,0,0:43:20	0/4:0,0,0,0,6:8:11:123,146,198,146,198,198,146,198,198,198,0,24,24,24,11	0/0:28,0,0,0,0:28:10	0/0:29,0,0,0,0:29:60	.	0/0:30,0,0,0,0:30:60	0/0:10,0,0,0,0:14:88:0,88,622,88,622,622,88,622,622,622,88,622,622,622,622	0/0:34,0,0,0,0:34:30	0/0:23,0,0,0,0:23:50	0/0:37,0,0,0,0:37:50	0/0:29,0,0,0,0:29:60	0/0:34,0,0,0,0:34:30	0/0:43,0,0,0,0:43:20	.	0/0:31,0,0,0,0:31:60	0/0:39,0,0,0,0:39:60	0/0:28,0,0,0,0:28:60	0/0:36,0,0,0,0:36:60	0/0:38,0,0,0,0:38:60	0/0:36,0,0,0,0:36:30	0/0:31,0,0,0,0:31:50	0/0:29,0,0,0,0:29:50	.	0/0:33,0,0,0,0:33:60	.	1/1:0,2,0,0,0:2:8:47,8,0,47,8,47,47,8,47,47,47,8,47,47,47	0/0:15,0,0,0,0:15:10	.


In this variant QUAL decreases because the haploids with no data have their PLs stripped. Those were already no-calls so AC/AN remain the same.

gatk-bot · 2024-04-02T14:41:11Z

Github actions tests reported job failures from actions build 8524189026
Failures in the following jobs:

Test Type	JDK	Job ID	Logs
integration	17.0.6+10	8524189026.11	logs
variantcalling	17.0.6+10	8524189026.2	logs
integration	17.0.6+10	8524189026.0	logs
unit	17.0.6+10	8524189026.12	logs
unit	17.0.6+10	8524189026.1	logs

gatk-bot · 2024-04-02T14:49:00Z

Github actions tests reported job failures from actions build 8524495307
Failures in the following jobs:

Test Type	JDK	Job ID	Logs
unit	17.0.6+10	8524495307.12	logs
integration	17.0.6+10	8524495307.11	logs
unit	17.0.6+10	8524495307.1	logs
variantcalling	17.0.6+10	8524495307.2	logs
integration	17.0.6+10	8524495307.0	logs

gatk-bot · 2024-04-02T21:13:27Z

Github actions tests reported job failures from actions build 8528936143
Failures in the following jobs:

Test Type	JDK	Job ID	Logs
variantcalling	17.0.6+10	8528936143.2	logs

gatk-bot · 2024-04-03T15:49:55Z

Github actions tests reported job failures from actions build 8541176894
Failures in the following jobs:

Test Type	JDK	Job ID	Logs
integration	17.0.6+10	8541176894.11	logs
variantcalling	17.0.6+10	8541176894.2	logs
integration	17.0.6+10	8541176894.0	logs

ldgauthier · 2024-04-03T20:29:38Z

From WARP JG tests:
branch NA12878 exome results
type TP FP FN RECALL PRECISION
SNP 17518 141 769 0.958 0.992
INDEL 314 91 89 0.779 0.775

develop NA12878 exome results
type TP FP FN RECALL PRECISION
SNP 17514 173 773 0.958 0.99
INDEL 310 91 93 0.769 0.773

Slight improvement!

A lot of QUAL scores change, which is to be expected. A few crappy variants disappear entirely, like this one:

#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	CHMI_CHMI3_Nex1	NA12878	NA12891	NA12892	NA19238	NA20845	NA20846	NA20847	NA20849	NA20850	NA20851	NA20852	NA20853	NA20854	NA20856	NA20858	NA20859	NA20861	NA20862	NA20866	NA20869	NA20870	NA20871	NA20872	NA20873	NA20874	NA20875	NA20876	NA20877	NA20878	NA20881	NA20885	NA20886	NA20887	NA20888	NA20889	NA20890	NA20891	NA20892	NA20893	NA20894	NA20895	NA20896	NA20897	NA20898	NA20899	NA20901	NA20902	NA20903	NA20904	NA20905	NA20906	NA20908	NA20910	NA20911	NA21086	NA21087	NA21088	NA21093	NA21095	NA21114	NA21124	NA21126	NA21129	NA21137
chrM	15929	.	A	G	38.97	PASS	AC=2;AF=0.016;AN=128;AS_BaseQRankSum=.;AS_FS=0.000;AS_FilterStatus=PASS;AS_InbreedingCoeff=0.4169;AS_MQ=60.00;AS_MQRankSum=.;AS_QD=31.42;AS_ReadPosRankSum=.;AS_SOR=0.693;AS_VQSLOD=5.8384;AS_culprit=AS_MQ;DP=2328;ExcessHet=0.0000;FS=0.000;InbreedingCoeff=0.4169;MLEAC=5;MLEAF=0.038;MQ=60.00;QD=32.95;SOR=1.609	GT:AD:DP:GQ:PL	0/0:98,0:98:40	0/0:314,0:314:40	0/0:684,0:684:40	0/0:440,0:440:40	0/0:4,0:4:0	0/0:4,0:4:0	0/0:4,0:4:0	0/0:4,0:4:0	0/0:4,0:4:0	0/0:6,0:6:0	0/0:4,0:4:0	0/0:4,0:4:0	0/0:1,0:1:0	0/0:5,0:5:0	0/0:4,0:4:0	0/0:5,0:5:00/0:4,0:4:0	0/0:4,0:4:0	0/0:4,0:4:0	0/0:5,0:5:0	0/0:4,0:4:0	0/0:33,0:33:40	0/0:4,0:4:0	0/0:4,0:4:0	0/0:19,0:19:40	0/0:5,0:5:0	0/0:4,0:4:0	0/0:2,0:2:0	0/0:3,0:3:0	0/0:2,0:2:00/0:4,0:4:0	1/1:0,1:1:3:35,3,0	0/0:1,0:1:0	0/0:9,0:9:0	0/0:0,0:0:0	0/0:4,0:4:0	0/0:4,0:4:0	0/0:4,0:4:0	0/0:4,0:4:0	0/0:5,0:5:0	0/0:2,0:2:0	0/0:9,0:9:20	0/0:4,0:4:0	0/0:6,0:6:0	0/0:4,0:4:0	0/0:5,0:5:0	0/0:1,0:1:0	0/0:4,0:4:0	0/0:5,0:5:0	0/0:5,0:5:0	0/0:3,0:3:0	0/0:1,0:1:0	0/0:4,0:4:0	0/0:4,0:4:0	0/0:4,0:4:0	0/0:5,0:5:0	0/0:4,0:4:0	0/0:5,0:5:0	0/0:1,0:1:0	0/0:6,0:6:0	0/0:2,0:2:0	0/0:118,0:118:40	0/0:4,0:4:0	0/0:401,0:401:40	0/0:2,0:2:0

Sadly a hom-var with RQQ (i.e. PL[0]) of 35 just shouldn't make it because of the prior, but all those GQ0 hom-refs had been giving it a boost.

There are a LOT of differences in the WES results that I'm working on systematically summarizing, but everything I've spot-checked looks reasonable.

Highlights from Picard variant_calling_summary_metrics for exome:
FILTERED_SNPS values differ. Value1: 14124 Value2: 15092 Changed by 968.0 (relative change of 0.06853582554517133)
PCT_DBSNP values differ. Value1: 0.785208 Value2: 0.786779 Changed by 0.0015709996223449707 (relative change of 0.0020007433045657057)
DBSNP_TITV values differ. Value1: 3.265418 Value2: 3.281538 Changed by 0.016119999999999912 (relative change of 0.004936580860398243)
NOVEL_TITV values differ. Value1: 2.38526 Value2: 2.4175 Changed by 0.032239999999999824 (relative change of 0.01351634622640711)
It's a pretty big difference in filtered SNPs, but the Ti/Tv values improve (keeping in mind we're looking at exome regions)

I found an issue with the Picard variant calling detail metrics, so I don't trust the PCT_GQ0 values. With our low coverage exome data it makes a pretty significant difference in the unfiltered callrate, so we should point that out in the release notes.

gatk-bot · 2024-04-03T21:18:26Z

Github actions tests reported job failures from actions build 8545290623
Failures in the following jobs:

Test Type	JDK	Job ID	Logs
integration	17.0.6+10	8545290623.11	logs
variantcalling	17.0.6+10	8545290623.2	logs
integration	17.0.6+10	8545290623.0	logs

ldgauthier · 2024-04-04T14:40:50Z

WGS NA12878 results (over exome intervals)

test.summary.tsv
type TP FP FN RECALL PRECISION
SNP 18123 77 164 0.991 0.996
INDEL 395 7 8 0.98 0.983

truth.summary.tsv
type TP FP FN RECALL PRECISION
SNP 18138 84 149 0.992 0.995
INDEL 395 7 8 0.98 0.983

Pretty darn close to the same (and better than exomes -- we must still be using shorty exome reads? Because of crappy old 1000G data?)

Comparing WGS metrics, number of variants went down slightly, (esp. singletons), but that's because of the things buoyed up by GQ0s (value1 is expected, value2 is actual). A few selected metrics:
PCT_DBSNP values differ. Value1: 0.785048 Value2: 0.790694
NOVEL_TITV values differ. Value1: 1.975381 Value2: 1.99816
Both good!

PCT_DBSNP_INDELS values differ. Value1: 0.688828 Value2: 0.68689 Changed by -0.0019379854202270508 (relative change of -0.0028134533500118026)
Not good, but not bad if it's just 0.28%

For 4.5.0.0, callrate for VQSR-filtered WGS is 100%, i.e. there are no no-calls. In this PR the WGS callrate for our 30X (PCR-free?) whole genomes drops to about 95% since there are some low coverage sites and assembly failures.

Number of variants filtered for ExcessHet is unchanged in WGS and there's a <1% change in # of PASS sites because the QUAL and QD change a bit in some cases

gatk-bot · 2024-04-05T13:19:58Z

Github actions tests reported job failures from actions build 8570036475
Failures in the following jobs:

Test Type	JDK	Job ID	Logs
integration	17.0.6+10	8570036475.11	logs
integration	17.0.6+10	8570036475.0	logs

jamesemery

Mostly nit-picky comments, however i think you disabled some tests again!

More broadly i think this branch needs a better title/documentation somewhere of what the actual change is and what its consequences are. "Fix for GGVCFs --all-sites mode" is not informative since as far as i can tell the greedy behavior of downgrading ggvcf alleles and some of the other changes that result in stripping annotations are not related to all-sites mode at all. It needs to be clear that this strips annotations from 0GQ, 0PL genotypes and that can sometimes impact the QUAL calculations (admittedly by a minor factor, though your WARP tests seem to indicate its relevant). I'm not necessarily suggesting a blogpost but when David writes the patchnotes there should probably be a few sentences about the expected outcome.

I cannot really comment to how significant the WARP changes are... they look small in general and I'm not going to hold this up as we know anything that impacts the QUAL will cause jitter. Philosophically is this an acceptable change? Was it a mistake before that the annotations and QUALs were counting 0/0 nocalls that were not labeled as 0/0 nocalls and this what its doing now is more correct even though it might infinitesimally make some things worse for specific samples? Twitter probably thinks so...

jamesemery · 2024-04-05T13:51:36Z

src/testUtils/java/org/broadinstitute/hellbender/testutils/VariantContextTestUtils.java

+                + actual.stream().map(Object::toString).collect(Collectors.joining("\n","actual:\n","\n"))
+            +  expected.stream().map(Object::toString).collect(Collectors.joining("\n","expected:\n","\n")));
+        for (int i = 0; i < actual.size(); i++) {
+            assertion.accept(actual.get(i), expected.get(i));


I know this was moved from elsewhere but this is a minor nit, but probably include a more interesting message about the elemnt that mismatches and where it is in the list.

This is why I never refactor anything.

jamesemery · 2024-04-05T13:54:55Z

src/main/java/org/broadinstitute/hellbender/engine/VariantLocusWalker.java

+                                    new ReadsContext(reads, variantInterval, readFilter),
+                                    new ReferenceContext(reference, variantInterval),
+                                    new FeatureContext(features, variantInterval));
+                        } catch (final IllegalStateException e) {


Nice, though why specifically only IllegalStateException? Would we not want to wrap all exceptions?

There's a GGVCFs test that looks for a UserException in a specific case. In my experience it's the IllegalStateExceptions that are the most annoying. We can always add more later.

jamesemery · 2024-04-05T14:02:18Z

src/main/java/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFsEngine.java

@@ -494,7 +495,7 @@ static List<Genotype> cleanupGenotypeAnnotations(final VariantContext vc, final
     *  Does this genotype look like it has no reads and should be excluded from annotations?
     */
    static boolean excludeFromAnnotations(Genotype oldGT) {
-        return oldGT.isHomRef() && !oldGT.hasPL()
+        return (oldGT.isHomRef() || oldGT.isNoCall())


EXTREMELY minor comment...
(oldGT.hasDP() && oldGT.getDP() == 0) || !oldGT.hasDP())
-> !oldGT.hasDP() || oldGT.getDP() == 0

Done

This method is probably on the chopping block for the refactor

jamesemery · 2024-04-05T14:13:50Z

...va/org/broadinstitute/hellbender/tools/walkers/variantutils/PosteriorProbabilitiesUtils.java

-                        Utils.listFromPrimitives(GenotypeLikelihoods.fromLog10Likelihoods(posteriors.get(genoIdx)).getAsPLs()));
+                            Utils.listFromPrimitives(GenotypeLikelihoods.fromLog10Likelihoods(posteriors.get(genoIdx)).getAsPLs()));
+                //TODO: refactor me -- this is to make up for the GGVCFs changes fixing GQ0 hom-refs
+                if (!builder.makeWithShallowCopy().hasPL()) {


this one is in the path of a lot of tools (HC M2 all of the genotypers) from what I could see. So if there is no PL when calculating the posterior probabilities for the genotypes we give it a score anyway so it gets included in the QUAL score calculations?

Did you check using IntelliJ? It has a fairly generic name, but it's just in CalculateGenotypePosteriors and a HaplotypeCaller GVCF feature I tried and ought to deprecate because it actually made for bigger GVCFs.

I don't believe M2 touches this at all. You're probably thinking of the posteriors in the AlleleFrequency Calculator

(Those numbers admittedly don't d add up, but I'm not hiding anything. The other hits are in the PosteriorProbabilityUtilsUnitTest)

jamesemery · 2024-04-05T14:24:40Z

src/main/java/org/broadinstitute/hellbender/utils/variant/GATKVariantContextUtils.java

@@ -314,6 +314,15 @@ public static void makeGenotypeCall(final int ploidy,
        if(originalGT == null && assignmentMethod == GenotypeAssignmentMethod.BEST_MATCH_TO_ORIGINAL) {
            throw new IllegalArgumentException("original GT cannot be null if assignmentMethod is BEST_MATCH_TO_ORIGINAL");
        }
+        //only do this if we're not no-calling so CombineGVCFs and GenomicsDB keep attributes
+        if (assignmentMethod != GenotypeAssignmentMethod.SET_TO_NO_CALL && (originalGT.isHomRef() || originalGT.isNoCall()) && originalGT.hasGQ() && originalGT.getGQ() == 0) {


its intentional here that this can be overridden if we are in most of the below genotyping modes?

in ALL cases, downgrade GQ0 + DP0 calls to no-calls but if there is depth maybe let it be computed to something else depending on the genotyping mode?

jamesemery · 2024-04-05T14:32:31Z

src/main/java/org/broadinstitute/hellbender/utils/variant/GATKVariantContextUtils.java

@@ -314,6 +314,15 @@ public static void makeGenotypeCall(final int ploidy,
        if(originalGT == null && assignmentMethod == GenotypeAssignmentMethod.BEST_MATCH_TO_ORIGINAL) {
            throw new IllegalArgumentException("original GT cannot be null if assignmentMethod is BEST_MATCH_TO_ORIGINAL");
        }
+        //only do this if we're not no-calling so CombineGVCFs and GenomicsDB keep attributes


If you are really looking for a refactor... this method is a spiderweb of death... you might consider refactoring it to use a switch statement on the ployidy mode so its at least a little more parseable...

jamesemery · 2024-04-05T14:35:54Z

src/test/java/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFsIntegrationTest.java

    @DataProvider(name = "gvcfsToGenotype")
    public Object[][] gvcfsToGenotype() {
        return new Object[][]{
+/*


disabling tests again?!?!?

to reduce the likelihood of this happening i suggest you comment out these tests with // line comments, that way its crystal clear for you/the reveiewer what tests are gone.

src/test/java/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFsIntegrationTest.java

jamesemery · 2024-04-05T14:46:06Z

...titute/hellbender/tools/walkers/variantutils/CalculateGenotypePosteriorsIntegrationTest.java

@@ -83,7 +100,28 @@ public void testMissingPriors() throws IOException {
                        " --" + StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE +" false",
                Collections.singletonList(largeDir + "CalculateGenotypePosteriors/expectedCGP_testMissingPriors.vcf")
        );
-        spec.executeTest("testMissingPriors", this);
+        //spec.executeTest("testMissingPriors", this);


also i think the IntegrationTestspec is now dead and can be removed?

I couldn't figure out how to do the VC and genotypes check like we do for GGVCFs so I just put the exact match back. Next time I break it I'll switch to the assertMatchingVariantContexts

jamesemery · 2024-04-05T14:52:31Z

...s/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/multiSamples.GATK3expected.g.vcf

-20	899937	.	G	T,*	4886.09	.	AC=19,2;AF=0.731,0.077;AN=26;AS_BaseQRankSum=-1.000,.;AS_FS=0.000,0.000;AS_InbreedingCoeff=0.5390,0.3914;AS_MQ=40.57,0.00;AS_MQRankSum=-0.700,.;AS_QD=27.24,16.50;AS_ReadPosRankSum=0.000,.;AS_SOR=1.775,0.105;BaseQRankSum=-9.670e-01;ClippingRankSum=0.00;DP=126;ExcessHet=0.0000;FS=0.000;InbreedingCoeff=0.5260;MLEAC=29,2;MLEAF=1.00,0.077;MQ=39.50;MQRankSum=-6.740e-01;QD=28.20;RAW_MQ=184116.00;ReadPosRankSum=0.00;SOR=1.697	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,3,0:3:9:1|1:899928_G_C:135,9,0,135,9,135	1/1:0,15,0:15:45:1|1:899928_G_C:675,45,0,675,45,675	1/1:0,15,0:15:43:1|1:899928_G_C:633,43,0,633,43,633	./.:0,0,0:0:0:.:.:0,0,0,0,0,0	./.:0,0,0:0:0:.:.:0,0,0,0,0,0	./.:0,0,0	./.:1,0,0:1:0:.:.:0,0,0,0,0,0	1/1:0,8,0:8:24:1|1:899928_G_C:360,24,0,360,24,360	2/2:0,0,1:1:3:1|1:899928_G_C:45,45,45,3,3,0	./.:1,0,0:1:0:.:.:0,0,0,0,0,0	./.:2,0,0:2:0:.:.:0,0,0,0,0,0	./.:1,0,0:1:0:.:.:0,0,0,0,0,0	1/1:0,6,0:6:18:1|1:899928_G_C:270,18,0,270,18,270	./.:0,0,0	0/1:2,2,0:4:78:0|1:899928_G_C:78,0,282,84,288,372	./.:0,0,0:0:0:.:.:0,0,0,0,0,0	1/1:0,48,0:48:99:1|1:899928_G_C:2194,147,0,2194,147,2194	1/1:0,4,0:4:12:1|1:899928_G_C:180,12,0,180,12,180	./.:2,0,0:2:0:.:.:0,0,0,0,0,0	0/0:7,0,0:7:9:.:.:0,9,182,9,182,182	1/1:0,4,0:4:12:1|1:899928_G_C:180,12,0,180,12,180	1/1:0,2,0:2:6:1|1:899928_G_C:90,6,0,90,6,90	./.:0,0,0:0:0:.:.:0,0,0,0,0,0	0/0:1,0,0:1:3:.:.:0,3,36,3,36,36
-20	899938	.	G	C,*	4882.54	.	AC=19,2;AF=0.731,0.077;AN=26;AS_BaseQRankSum=-1.400,.;AS_FS=0.000,0.000;AS_InbreedingCoeff=0.5553,0.4090;AS_MQ=40.66,0.00;AS_MQRankSum=-0.700,.;AS_QD=25.00,16.50;AS_ReadPosRankSum=0.000,.;AS_SOR=1.900,0.105;BaseQRankSum=-1.383e+00;ClippingRankSum=0.00;DP=124;ExcessHet=0.0000;FS=0.000;InbreedingCoeff=0.5362;MLEAC=29,2;MLEAF=1.00,0.077;MQ=39.58;MQRankSum=-6.740e-01;QD=29.56;RAW_MQ=183275.00;ReadPosRankSum=0.00;SOR=1.811	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,3,0:3:9:1|1:899928_G_C:135,9,0,135,9,135	1/1:0,14,0:14:45:1|1:899928_G_C:675,45,0,675,45,675	1/1:0,15,0:15:43:1|1:899928_G_C:633,43,0,633,43,633	./.:0,0,0:0:0:.:.:0,0,0,0,0,0	./.:0,0,0:0:0:.:.:0,0,0,0,0,0	./.:0,0,0	./.:1,0,0:1:0:.:.:0,0,0,0,0,0	1/1:0,8,0:8:24:1|1:899928_G_C:360,24,0,360,24,360	2/2:0,0,1:1:3:1|1:899928_G_C:45,45,45,3,3,0	./.:1,0,0:1:0:.:.:0,0,0,0,0,0	./.:2,0,0:2:0:.:.:0,0,0,0,0,0	./.:1,0,0:1:0:.:.:0,0,0,0,0,0	1/1:0,6,0:6:18:1|1:899928_G_C:270,18,0,270,18,270	./.:0,0,0	0/1:2,2,0:4:78:0|1:899928_G_C:78,0,282,84,288,372	./.:0,0,0:0:0:.:.:0,0,0,0,0,0	1/1:0,48,0:48:99:1|1:899928_G_C:2194,147,0,2194,147,2194	1/1:0,4,0:4:12:1|1:899928_G_C:180,12,0,180,12,180	./.:2,0,0:2:0:.:.:0,0,0,0,0,0	0/0:6,0,0:6:15:.:.:0,15,225,15,225,225	1/1:0,4,0:4:12:1|1:899928_G_C:180,12,0,180,12,180	1/1:0,2,0:2:6:1|1:899928_G_C:90,6,0,90,6,90	./.:0,0,0:0:0:.:.:0,0,0,0,0,0	0/0:1,0,0:1:3:.:.:0,3,36,3,36,36
-20	899942	.	G	A	4913.79	.	AC=19;AF=0.792;AN=24;AS_BaseQRankSum=0.400;AS_FS=0.000;AS_InbreedingCoeff=0.5567;AS_MQ=44.39;AS_MQRankSum=-0.300;AS_QD=30.62;AS_ReadPosRankSum=-1.500;AS_SOR=1.893;BaseQRankSum=0.493;ClippingRankSum=0.00;DP=148;ExcessHet=0.0000;FS=0.000;InbreedingCoeff=0.4850;MLEAC=30;MLEAF=1.00;MQ=43.13;MQRankSum=-2.530e-01;QD=28.17;RAW_MQ=264157.00;ReadPosRankSum=-1.501e+00;SOR=1.923	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,3:3:9:1|1:899928_G_C:135,9,0	1/1:0,15:15:45:1|1:899928_G_C:636,45,0	1/1:0,16:16:45:1|1:899928_G_C:636,45,0	./.:0,0:0:0:.:.:0,0,0	./.:0,0:0:0:.:.:0,0,0	./.:0,0	./.:1,0:1:0:.:.:0,0,0	1/1:0,9:9:27:1|1:899928_G_C:366,27,0	./.:3,0:3:0:.:.:0,0,0	./.:0,0:0:0:.:.:0,0,0	./.:2,0:2:0:.:.:0,0,0	./.:1,0:1:0:.:.:0,0,0	1/1:0,7:7:19:1|1:899928_G_C:273,19,0	./.:0,0	0/1:2,8:10:88:0|1:899928_G_C:88,0,274	./.:0,0:0:0:.:.:0,0,0	1/1:0,58:58:99:1|1:899928_G_C:2217,159,0	1/1:0,5:5:13:1|1:899928_G_C:183,13,0	./.:2,0:2:0:.:.:0,0,0	0/0:5,0:5:15:.:.:0,15,178	1/1:0,7:7:16:1|1:899928_G_C:189,16,0	1/1:0,2:2:6:1|1:899928_G_C:90,6,0	./.:0,0:0:0:.:.:0,0,0	0/0:1,0:1:3:.:.:0,3,36
+20	899928	.	G	C	4944.58	.	AC=21;AF=0.808;AN=26;AS_BaseQRankSum=-1.400;AS_FS=0.000;AS_InbreedingCoeff=0.5339;AS_MQ=43.54;AS_MQRankSum=-0.700;AS_QD=25.36;AS_ReadPosRankSum=0.000;AS_SOR=1.863;BaseQRankSum=-1.383e+00;ClippingRankSum=0.00;DP=133;ExcessHet=0.0000;FS=0.000;InbreedingCoeff=0.5089;MLEAC=25;MLEAF=0.962;MQ=42.34;MQRankSum=-6.740e-01;QD=28.73;RAW_MQ=222270.00;ReadPosRankSum=0.00;SOR=1.781	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,3:3:9:1|1:899928_G_C:135,9,0	1/1:0,18:18:54:1|1:899928_G_C:767,54,0	1/1:0,15:15:45:1|1:899928_G_C:640,45,0	./.	./.	./.	./.	1/1:0,9:9:27:1|1:899928_G_C:370,27,0	1/1:0,1:1:3:1|1:899928_G_C:45,3,0	./.:1,0:1:0:.:.:0,0,0	./.:2,0:2:0:.:.:0,0,0	./.:3,0:3:0:.:.:0,0,0	1/1:0,5:5:15:1|1:899928_G_C:225,15,0	./.	0/1:2,2:4:78:0|1:899928_G_C:78,0,282	./.	1/1:0,51:51:99:1|1:899928_G_C:2229,153,0	1/1:0,3:3:9:1|1:899928_G_C:135,9,0	./.:2,0:2:0:.:.:0,0,0	0/0:7,0:7:21:.:.:0,21,236	1/1:0,4:4:12:1|1:899928_G_C:168,12,0	1/1:0,2:2:6:1|1:899928_G_C:90,6,0	./.	0/0:2,0:2:6:.:.:0,6,65


man this file is somewhat of a misnomer at this point huh...the QUALs changing here are expected?

can you explain why the quals change?

I changed the file name to take the gatk3 out.

QUALs are reduced after the [0,0,0] PLs are removed, which is expected and I confirmed with a little experiment in the AlleleFrequencyCalculatorUnitTest class. Each sample is weighted equally (for better or for worse) so the fact that it's a toss up what genotype the no-calls have is actually treated as evidence that this is a non-reference site (which is what the QUAL is measuring). But the ./. with PL=[0,0,0] had NO READS! So I want to take the PLs out so they don't influence the QUAL.

Some concrete examples
POS 899928 has QUAL 4973.12 -> 4944.58
POS 899933 has QUAL 31.97 -> 30.86

Gnarly doesn't have this problem because it uses a heuristic instead of the AlleleFrequencyCalculator and in this respect the heuristic does a little better

Set GGVCFs --all-sites GQ0 hom-refs to no-calls Set regular GGVCFs GQ0 hom-refs to no-calls (any DP, PL) for better AF/AN annotations Remove PLs in "no data" case where DP=0 for more accurate QUAL score

jamesemery

one more question, but now that the tests don't look like theyve been disabled its mostly a questoin of "correctness" and thats much more subjective

jamesemery · 2024-04-09T17:00:53Z

...nder/tools/walkers/GenotypeGVCFs/expected/gvcf.basepairResolution.includeNonVariantSites.vcf

@@ -9063,8 +9063,8 @@
 20	10008947	.	T	.	.	.	DP=24	GT:AD:DP:RGQ	0/0:24:24:12
 20	10008948	.	TA	T	1057.03	.	AC=2;AF=1.00;AN=2;DP=24;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=168.45;MQ0=0;QD=23.23;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,24:24:78:1071,78,0
 20	10008949	.	A	*	0	LowQual	AC=2;AF=1.00;AN=2;DP=24;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;QD=-0.00;SOR=0.693	GT:AD:DP:GQ:PL	1/1:0,24:24:78:1071,78,0
-20	10008950	.	A	.	.	.	DP=24	GT:AD:DP:RGQ	0/0:5:24:0


this case, where AD=5 and DP=24. we still want to downgrade it to a ./.?

Yep, that's gross. I don't want that. The AD representing the ALT is getting dropped because of our non-variant site format, but AD[1]=DP-AD[0]=19!!! That's a heck of a lot of ALT reads so I don't want to call this a hom-ref. This is a gross thing we shouldn't put any confidence in so I stand by the GQ0 no-call.

ldgauthier commented Mar 15, 2024

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droazen assigned jamesemery Mar 15, 2024

droazen requested a review from jamesemery March 15, 2024 18:05

ldgauthier commented Apr 2, 2024

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ldgauthier mentioned this pull request Apr 5, 2024

Fix GGVCFs typo #8742

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jamesemery reviewed Apr 5, 2024

View reviewed changes

Several GQ0 cleanup changes:

806024a

Set GGVCFs --all-sites GQ0 hom-refs to no-calls Set regular GGVCFs GQ0 hom-refs to no-calls (any DP, PL) for better AF/AN annotations Remove PLs in "no data" case where DP=0 for more accurate QUAL score

ldgauthier force-pushed the ldg_fix_all_sites_no_calls branch from 6d060ce to 806024a Compare April 8, 2024 14:18

jamesemery approved these changes Apr 9, 2024

View reviewed changes

ldgauthier changed the title ~~Fix for GGVCFs --all-sites mode~~ GGVCFs changes to revert "no data" calls to "./." and change GQ0 hom-refs to no-calls Apr 10, 2024

ldgauthier merged commit 7cdc985 into master Apr 10, 2024
17 checks passed

ldgauthier deleted the ldg_fix_all_sites_no_calls branch April 10, 2024 12:37

droazen mentioned this pull request Apr 10, 2024

Allow for GT to be a nocall if GQ and PL[0] are zero instead of homref in GenomicsDB #8759

Merged

This was referenced Jun 25, 2024

Restore 3 Gnarly tests #8892

Closed

Restore gnarly tests #8893

Merged

GGVCFs changes to revert "no data" calls to "./." and change GQ0 hom-refs to no-calls #8741

GGVCFs changes to revert "no data" calls to "./." and change GQ0 hom-refs to no-calls #8741

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