From 00ff83da2ebda414248ba65040b59b41f25296c7 Mon Sep 17 00:00:00 2001 From: Andrey Smirnov Date: Tue, 16 May 2023 16:03:14 -0400 Subject: [PATCH] Matched gCNV pipeline arguments to those that were shown to have good performance in running large exome cohorts. (#8234) --- scripts/cnv_wdl/cnv_common_tasks.wdl | 4 +- .../germline/cnv_germline_case_workflow.wdl | 6 +- .../germline/cnv_germline_cohort_workflow.wdl | 14 +- .../tools/copynumber/FilterIntervals.java | 4 +- .../GermlineCallingArgumentCollection.java | 4 +- ...neContigPloidyModelArgumentCollection.java | 4 +- ...mlineDenoisingModelArgumentCollection.java | 6 +- .../models/model_denoising_calling.py | 10 +- .../gcnvkernel/models/model_ploidy.py | 4 +- .../SAMPLE_0/log_c_emission_tc.tsv | 340 ++++++++--------- .../shard_0-calls/SAMPLE_0/log_q_c_tc.tsv | 340 ++++++++--------- .../SAMPLE_0/mu_denoised_copy_ratio_t.tsv | 340 ++++++++--------- .../shard_0-calls/SAMPLE_0/mu_psi_s_log__.tsv | 2 +- .../SAMPLE_0/mu_read_depth_s_log__.tsv | 2 +- .../shard_0-calls/SAMPLE_0/mu_z_su.tsv | 13 +- .../SAMPLE_0/std_denoised_copy_ratio_t.tsv | 340 ++++++++--------- .../SAMPLE_0/std_psi_s_log__.tsv | 2 +- .../SAMPLE_0/std_read_depth_s_log__.tsv | 2 +- .../shard_0-calls/SAMPLE_0/std_z_su.tsv | 13 +- .../shard_0-calls/calling_config.json | 4 +- .../shard_0-calls/denoising_config.json | 6 +- .../shard_0-model/calling_config.json | 4 +- .../shard_0-model/denoising_config.json | 6 +- .../shard_0-model/log_q_tau_tk.tsv | 340 ++++++++--------- .../shard_0-model/mu_W_tu.tsv | 344 +++++++++--------- .../shard_0-model/mu_ard_u_log__.tsv | 13 +- .../shard_0-model/mu_log_mean_bias_t.tsv | 340 ++++++++--------- .../shard_0-model/mu_psi_t_log__.tsv | 340 ++++++++--------- .../shard_0-model/std_W_tu.tsv | 344 +++++++++--------- .../shard_0-model/std_ard_u_log__.tsv | 13 +- .../shard_0-model/std_log_mean_bias_t.tsv | 340 ++++++++--------- .../shard_0-model/std_psi_t_log__.tsv | 340 ++++++++--------- 32 files changed, 1944 insertions(+), 1940 deletions(-) diff --git a/scripts/cnv_wdl/cnv_common_tasks.wdl b/scripts/cnv_wdl/cnv_common_tasks.wdl index 261d93346b0..9b5b4745815 100644 --- a/scripts/cnv_wdl/cnv_common_tasks.wdl +++ b/scripts/cnv_wdl/cnv_common_tasks.wdl @@ -158,8 +158,8 @@ task FilterIntervals { --maximum-mappability ~{default="1.0" maximum_mappability} \ --minimum-segmental-duplication-content ~{default="0.0" minimum_segmental_duplication_content} \ --maximum-segmental-duplication-content ~{default="0.5" maximum_segmental_duplication_content} \ - --low-count-filter-count-threshold ~{default="5" low_count_filter_count_threshold} \ - --low-count-filter-percentage-of-samples ~{default="90.0" low_count_filter_percentage_of_samples} \ + --low-count-filter-count-threshold ~{default="10" low_count_filter_count_threshold} \ + --low-count-filter-percentage-of-samples ~{default="50.0" low_count_filter_percentage_of_samples} \ --extreme-count-filter-minimum-percentile ~{default="1.0" extreme_count_filter_minimum_percentile} \ --extreme-count-filter-maximum-percentile ~{default="99.0" extreme_count_filter_maximum_percentile} \ --extreme-count-filter-percentage-of-samples ~{default="90.0" extreme_count_filter_percentage_of_samples} \ diff --git a/scripts/cnv_wdl/germline/cnv_germline_case_workflow.wdl b/scripts/cnv_wdl/germline/cnv_germline_case_workflow.wdl index 5135b0f8858..f097cc8068f 100644 --- a/scripts/cnv_wdl/germline/cnv_germline_case_workflow.wdl +++ b/scripts/cnv_wdl/germline/cnv_germline_case_workflow.wdl @@ -323,7 +323,7 @@ task DetermineGermlineContigPloidyCaseMode { --output ~{output_dir_} \ --output-prefix case \ --verbosity DEBUG \ - --mapping-error-rate ~{default="0.01" mapping_error_rate} \ + --mapping-error-rate ~{default="0.3" mapping_error_rate} \ --sample-psi-scale ~{default="0.0001" sample_psi_scale} tar c -C ~{output_dir_}/case-calls . | gzip -1 > case-contig-ploidy-calls.tar.gz @@ -423,11 +423,11 @@ task GermlineCNVCallerCaseMode { --output ~{output_dir_} \ --output-prefix case \ --verbosity DEBUG \ - --p-alt ~{default="1e-6" p_alt} \ + --p-alt ~{default="5e-4" p_alt} \ --cnv-coherence-length ~{default="10000.0" cnv_coherence_length} \ --max-copy-number ~{default="5" max_copy_number} \ --mapping-error-rate ~{default="0.01" mapping_error_rate} \ - --sample-psi-scale ~{default="0.0001" sample_psi_scale} \ + --sample-psi-scale ~{default="0.01" sample_psi_scale} \ --depth-correction-tau ~{default="10000.0" depth_correction_tau} \ --copy-number-posterior-expectation-mode ~{default="HYBRID" copy_number_posterior_expectation_mode} \ --active-class-padding-hybrid-mode ~{default="50000" active_class_padding_hybrid_mode} \ diff --git a/scripts/cnv_wdl/germline/cnv_germline_cohort_workflow.wdl b/scripts/cnv_wdl/germline/cnv_germline_cohort_workflow.wdl index fecc8dad08b..03140d85cb2 100644 --- a/scripts/cnv_wdl/germline/cnv_germline_cohort_workflow.wdl +++ b/scripts/cnv_wdl/germline/cnv_germline_cohort_workflow.wdl @@ -485,8 +485,8 @@ task DetermineGermlineContigPloidyCohortMode { --output ~{output_dir_} \ --output-prefix ~{cohort_entity_id} \ --verbosity DEBUG \ - --mean-bias-standard-deviation ~{default="0.01" mean_bias_standard_deviation} \ - --mapping-error-rate ~{default="0.01" mapping_error_rate} \ + --mean-bias-standard-deviation ~{default="1" mean_bias_standard_deviation} \ + --mapping-error-rate ~{default="0.3" mapping_error_rate} \ --global-psi-scale ~{default="0.001" global_psi_scale} \ --sample-psi-scale ~{default="0.0001" sample_psi_scale} @@ -599,15 +599,15 @@ task GermlineCNVCallerCohortMode { --output ~{output_dir_} \ --output-prefix ~{cohort_entity_id} \ --verbosity DEBUG \ - --p-alt ~{default="1e-6" p_alt} \ - --p-active ~{default="1e-2" p_active} \ + --p-alt ~{default="5e-4" p_alt} \ + --p-active ~{default="1e-1" p_active} \ --cnv-coherence-length ~{default="10000.0" cnv_coherence_length} \ --class-coherence-length ~{default="10000.0" class_coherence_length} \ --max-copy-number ~{default="5" max_copy_number} \ - --max-bias-factors ~{default="5" max_bias_factors} \ + --max-bias-factors ~{default="6" max_bias_factors} \ --mapping-error-rate ~{default="0.01" mapping_error_rate} \ - --interval-psi-scale ~{default="0.001" interval_psi_scale} \ - --sample-psi-scale ~{default="0.0001" sample_psi_scale} \ + --interval-psi-scale ~{default="0.01" interval_psi_scale} \ + --sample-psi-scale ~{default="0.01" sample_psi_scale} \ --depth-correction-tau ~{default="10000.0" depth_correction_tau} \ --log-mean-bias-standard-deviation ~{default="0.1" log_mean_bias_standard_deviation} \ --init-ard-rel-unexplained-variance ~{default="0.1" init_ard_rel_unexplained_variance} \ diff --git a/src/main/java/org/broadinstitute/hellbender/tools/copynumber/FilterIntervals.java b/src/main/java/org/broadinstitute/hellbender/tools/copynumber/FilterIntervals.java index eb3e74e7a6c..1e1fb21b8da 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/copynumber/FilterIntervals.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/copynumber/FilterIntervals.java @@ -229,7 +229,7 @@ public final class FilterIntervals extends CommandLineProgram { minValue = 0, optional = true ) - private int lowCountFilterCountThreshold = 5; + private int lowCountFilterCountThreshold = 10; @Argument( doc = "Percentage-of-samples parameter for the low-count filter. Intervals with a count " + @@ -241,7 +241,7 @@ public final class FilterIntervals extends CommandLineProgram { maxValue = 100., optional = true ) - private double lowCountFilterPercentageOfSamples = 90.; + private double lowCountFilterPercentageOfSamples = 50.; @Argument( doc = "Minimum-percentile parameter for the extreme-count filter. Intervals with a count " + diff --git a/src/main/java/org/broadinstitute/hellbender/tools/copynumber/arguments/GermlineCallingArgumentCollection.java b/src/main/java/org/broadinstitute/hellbender/tools/copynumber/arguments/GermlineCallingArgumentCollection.java index 61932bfa55d..ec9be60039e 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/copynumber/arguments/GermlineCallingArgumentCollection.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/copynumber/arguments/GermlineCallingArgumentCollection.java @@ -37,7 +37,7 @@ public final class GermlineCallingArgumentCollection implements Serializable { maxValue = 1., optional = true ) - private double pAlt = 1e-6; + private double pAlt = 5e-4; @Argument( doc = "Prior probability of treating an interval as CNV-active (in a CNV-active domains, all " + @@ -47,7 +47,7 @@ public final class GermlineCallingArgumentCollection implements Serializable { maxValue = 1., optional = true ) - private double pActive = 1e-2; + private double pActive = 1e-1; @Argument( doc = "Coherence length of CNV events (in the units of bp).", diff --git a/src/main/java/org/broadinstitute/hellbender/tools/copynumber/arguments/GermlineContigPloidyModelArgumentCollection.java b/src/main/java/org/broadinstitute/hellbender/tools/copynumber/arguments/GermlineContigPloidyModelArgumentCollection.java index fd7cd7f6d93..636683b506b 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/copynumber/arguments/GermlineContigPloidyModelArgumentCollection.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/copynumber/arguments/GermlineContigPloidyModelArgumentCollection.java @@ -27,7 +27,7 @@ public final class GermlineContigPloidyModelArgumentCollection implements Serial minValue = 0., optional = true ) - private double meanBiasStandardDeviation = 0.01; + private double meanBiasStandardDeviation = 1.; @Argument( doc = "Typical mapping error rate.", @@ -36,7 +36,7 @@ public final class GermlineContigPloidyModelArgumentCollection implements Serial maxValue = 1., optional = true ) - private double mappingErrorRate = 0.01; + private double mappingErrorRate = 0.3; @Argument( doc = "Prior scale of contig coverage unexplained variance. If a single sample is provided, " + diff --git a/src/main/java/org/broadinstitute/hellbender/tools/copynumber/arguments/GermlineDenoisingModelArgumentCollection.java b/src/main/java/org/broadinstitute/hellbender/tools/copynumber/arguments/GermlineDenoisingModelArgumentCollection.java index d3ea880ce22..26b10f10998 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/copynumber/arguments/GermlineDenoisingModelArgumentCollection.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/copynumber/arguments/GermlineDenoisingModelArgumentCollection.java @@ -61,7 +61,7 @@ public enum CopyNumberPosteriorExpectationMode { minValue = 0, optional = true ) - private int maxBiasFactors = 5; + private int maxBiasFactors = 6; @Argument( doc = "Typical mapping error rate.", @@ -78,7 +78,7 @@ public enum CopyNumberPosteriorExpectationMode { minValue = 0., optional = true ) - private double intervalPsiScale = 0.001; + private double intervalPsiScale = 0.01; @Argument( doc = "Typical scale of sample-specific correction to the unexplained variance.", @@ -86,7 +86,7 @@ public enum CopyNumberPosteriorExpectationMode { minValue = 0., optional = true ) - private double samplePsiScale = 0.0001; + private double samplePsiScale = 0.01; @Argument( doc = "Precision of read depth pinning to its global value.", diff --git a/src/main/python/org/broadinstitute/hellbender/gcnvkernel/models/model_denoising_calling.py b/src/main/python/org/broadinstitute/hellbender/gcnvkernel/models/model_denoising_calling.py index b67c7c194a8..63ef4f9e86f 100644 --- a/src/main/python/org/broadinstitute/hellbender/gcnvkernel/models/model_denoising_calling.py +++ b/src/main/python/org/broadinstitute/hellbender/gcnvkernel/models/model_denoising_calling.py @@ -36,10 +36,10 @@ class DenoisingModelConfig: _q_c_expectation_modes = ['map', 'exact', 'hybrid'] def __init__(self, - max_bias_factors: int = 5, + max_bias_factors: int = 6, mapping_error_rate: float = 0.01, - psi_t_scale: float = 0.001, - psi_s_scale: float = 0.0001, + psi_t_scale: float = 0.01, + psi_s_scale: float = 0.01, depth_correction_tau: float = 10000.0, log_mean_bias_std: float = 0.1, init_ard_rel_unexplained_variance: float = 0.1, @@ -202,8 +202,8 @@ def from_json_file(json_file: str) -> 'DenoisingModelConfig': class CopyNumberCallingConfig: """Configuration of the copy number caller.""" def __init__(self, - p_alt: float = 1e-6, - p_active: float = 1e-3, + p_alt: float = 5e-4, + p_active: float = 0.1, cnv_coherence_length: float = 10000.0, class_coherence_length: float = 10000.0, max_copy_number: int = 5, diff --git a/src/main/python/org/broadinstitute/hellbender/gcnvkernel/models/model_ploidy.py b/src/main/python/org/broadinstitute/hellbender/gcnvkernel/models/model_ploidy.py index 9b18bcb3639..fd50776420f 100644 --- a/src/main/python/org/broadinstitute/hellbender/gcnvkernel/models/model_ploidy.py +++ b/src/main/python/org/broadinstitute/hellbender/gcnvkernel/models/model_ploidy.py @@ -24,10 +24,10 @@ class PloidyModelConfig: """Germline contig ploidy model hyper-parameters.""" def __init__(self, contig_ploidy_prior_map: Dict[str, np.ndarray] = None, - mean_bias_sd: float = 1e-2, + mean_bias_sd: float = 1., psi_j_scale: float = 1e-3, psi_s_scale: float = 1e-4, - mapping_error_rate: float = 1e-2): + mapping_error_rate: float = 0.3): """Initializer. Args: diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-calls/SAMPLE_0/log_c_emission_tc.tsv b/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-calls/SAMPLE_0/log_c_emission_tc.tsv index f8b2f8edc8f..6d0a4b2dbd1 100644 --- a/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-calls/SAMPLE_0/log_c_emission_tc.tsv +++ b/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-calls/SAMPLE_0/log_c_emission_tc.tsv @@ -1,172 +1,172 @@ @RG ID:GATKCopyNumber SM:SAMPLE_000 COPY_NUMBER_0 COPY_NUMBER_1 COPY_NUMBER_2 COPY_NUMBER_3 COPY_NUMBER_4 COPY_NUMBER_5 --3718.6283251446744 -88.75162669552559 -5.892405769638854 -28.622827280547387 -71.17816858307162 -116.93585145887775 --9454.442599242697 -90.06709385868929 -7.118479100485037 -32.595755210303466 -73.87391033784156 -116.15496961410193 --3398.390150797672 -69.67846350395715 -6.1819311977814575 -31.24990831453078 -71.52801754721553 -113.46157362803358 --4.454863134361248 -2.243951136248023 -3.5329924499361143 -6.200202171896734 -9.57708329639005 -13.36648258616691 --2619.368205697241 -83.36144421665982 -5.716369177424653 -30.417536292277127 -76.81506842213334 -127.58861902053708 --1392.0544015185974 -56.23703472106425 -5.031435824393768 -27.89423322653279 -68.40480740885044 -113.15890558377333 --719.9688140468317 -41.192572741863415 -4.456998969031516 -19.130066350227054 -47.9771574853105 -81.18651019564095 --5363.973710716001 -92.88082420543512 -6.435660403911864 -39.90409437686533 -93.43931694045698 -148.98156274170407 --5978.946758593645 -41.087056378534974 -6.840810258156937 -15.316269287314615 -29.722470128922065 -44.50402612390527 --2840.43458764683 -71.47403579851361 -5.523760447810765 -25.834963126918467 -62.304340206810004 -101.28747571428939 --14.03640767442917 -5.979772113361577 -3.170395771727784 -2.6112128714784317 -3.2819428631097467 -4.711312407031316 --428.47574281736365 -30.73510106661839 -4.299374618577287 -14.083784558205167 -34.52880081094867 -58.57436465422577 --3614.3785309861514 -76.14666378666253 -6.125392904069521 -29.11542158530581 -68.38489314204614 -109.71418591608756 --70.67274991149972 -9.683230385192099 -3.224187409487037 -7.33435211485856 -15.491692484889192 -25.499875737299874 --16.707008128134483 -4.4157090089093 -2.6299473105612323 -4.338557356176541 -7.7488303633941715 -12.128940165787448 --17369.97581738282 -76.56173569318827 -7.899034628286783 -33.391453131151614 -70.79577719270958 -108.10986507095623 --46.69590636349095 -6.934453711146105 -3.105441087633158 -7.399670997754839 -15.083766600956086 -24.47328288469842 --767.7752581084734 -36.548333795225986 -4.641758877413283 -16.858619473031542 -39.315205915438895 -64.1475285943682 --414.15227028844174 -27.558712292620577 -4.3382708107650885 -12.063018891434792 -27.827273884403418 -45.84714720894375 --198.27292863833952 -18.58289757742494 -4.102620664461279 -8.073299968926612 -17.213873123215485 -27.967375660455883 --18319.650110216513 -91.49360035340051 -7.611192771012172 -34.884767417886174 -76.88104770739054 -119.22253681439028 --2596.3282814440945 -74.29388183783644 -5.745036320273153 -27.44177732310905 -66.99369886677539 -109.66792810639963 --1392.742231375302 -56.38828159096078 -4.940115307993056 -23.020460887413996 -57.025520505920646 -94.68283825623865 --213.06191501580025 -19.153658662261265 -3.70182637575352 -12.314109944658691 -29.268991680401456 -49.695163878364795 --804.1319794142184 -38.23994808427808 -4.674481122399277 -18.698645161647956 -44.03650486383667 -72.0887364344971 --321.0399175126818 -27.565794090775434 -3.9620290753788456 -11.585643409069643 -29.315393626211993 -50.93749962557463 --79.61586656211931 -9.859356651566813 -3.3732030221961358 -7.391712397134844 -14.919008986635774 -23.782484375038443 --11.832499999878035 -3.54763361497253 -2.6029213237950093 -4.302625341670162 -7.329698977103919 -11.12660060060891 --278.81892839633554 -19.485545479956397 -4.192819772196645 -14.84204496062938 -33.07635843301273 -53.77537003972702 --1983.6988642082206 -68.98197539743848 -5.671532590789305 -19.36954202612077 -49.24619681782818 -82.526662397579 --446.5144562871017 -36.9337999280002 -4.37613562325976 -12.092497221719062 -32.74618693391674 -58.37816545923097 --2815.512418717087 -67.12448963892297 -5.837843563257852 -28.380061893061704 -66.21994310302159 -106.16325318151405 --3124.0371589412357 -60.84959592974673 -6.254389200877464 -30.615189036180908 -68.00384856848444 -106.49494912795603 --1146.2184850240744 -39.72236901214548 -5.303479155168587 -24.59058968953353 -54.937432561284744 -87.13663069011346 --82.16409507491403 -11.629503783304168 -3.183562530518774 -6.936224963150947 -15.556383024761299 -26.538930207850143 --1658.737079689237 -62.75260373708731 -5.1874732094276315 -26.14682466575882 -64.88127651028235 -107.60021929865417 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baa6ea0126a..d9245516214 100644 --- a/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-calls/SAMPLE_0/mu_denoised_copy_ratio_t.tsv +++ b/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-calls/SAMPLE_0/mu_denoised_copy_ratio_t.tsv @@ -2,173 +2,173 @@ @CO dtype:float64 @RG ID:GATKCopyNumber SM:SAMPLE_000 VALUE_0 -2.017724654993046 -1.9518253192990103 -1.918840904380183 -1.9844114397743593 -1.9848056624827992 -1.9800286686658837 -2.0190661664260765 -1.9324016001076856 -1.987402320685559 -1.9898374834519827 -3.9903711947307654 -2.0899485746110593 -1.9769267618830488 -2.175028119750007 -2.6069979158686065 -1.8690661521413166 -2.129807600406914 -1.97420890823427 -2.118948806669572 -2.235154627725029 -1.9059454920604764 -2.012339832410029 -1.9836520573218988 -2.0357403431355645 -2.0124303342877687 -2.1291804628488333 -2.15046895592795 -2.565240862309793 -1.961309612781913 -2.1092867679566742 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b/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-calls/SAMPLE_0/mu_read_depth_s_log__.tsv index fdcaa46a637..c96a77a10a3 100644 --- a/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-calls/SAMPLE_0/mu_read_depth_s_log__.tsv +++ b/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-calls/SAMPLE_0/mu_read_depth_s_log__.tsv @@ -2,4 +2,4 @@ @CO dtype:float64 @RG ID:GATKCopyNumber SM:SAMPLE_000 VALUE_0 -6.042016629968644 +6.046959920320962 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-calls/SAMPLE_0/mu_z_su.tsv b/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-calls/SAMPLE_0/mu_z_su.tsv index abec84891c6..3d86b49fe40 100644 --- a/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-calls/SAMPLE_0/mu_z_su.tsv +++ b/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-calls/SAMPLE_0/mu_z_su.tsv @@ -1,9 +1,10 @@ -@CO shape:(5,) +@CO shape:(6,) @CO dtype:float64 @RG ID:GATKCopyNumber SM:SAMPLE_000 VALUE_0 -1.163024900422762 -0.68371093777678 --1.7967589464045208 --0.08582109828734125 --0.05480055588913115 +-0.012115853878657032 +-1.0135477723806217 +0.8780923681315713 +1.750551551168998 +-0.6475298304403772 +0.13033304429958514 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-calls/SAMPLE_0/std_denoised_copy_ratio_t.tsv b/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-calls/SAMPLE_0/std_denoised_copy_ratio_t.tsv index 7cbc82696a3..702e2774363 100644 --- a/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-calls/SAMPLE_0/std_denoised_copy_ratio_t.tsv +++ b/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-calls/SAMPLE_0/std_denoised_copy_ratio_t.tsv @@ -2,173 +2,173 @@ @CO dtype:float64 @RG ID:GATKCopyNumber SM:SAMPLE_000 VALUE_0 -0.1595961689729248 -0.15499215090042814 -0.15048141661204137 -0.17624305278578142 -0.15063296948807833 -0.14665509589128706 -0.13967022136593862 -0.14111099753427125 -0.1943366702546657 -0.15387953787239878 -0.4051097183226438 -0.18716295450978568 -0.147553853498754 -0.21346632965957169 -0.21987396690853564 -0.15833706103309586 -0.16823144671732895 -0.16458610177197233 -0.21721835917063984 -0.2296975682083221 -0.14361604850266968 -0.16697803268067613 -0.14575305016756998 -0.15070398481739786 -0.1693912478930392 -0.15792727899056921 -0.2090446250232529 -0.2462779071442959 -0.19389505150451636 -0.17017485498268242 -0.16525922013227548 -0.15273862733451815 -0.1447438516588371 -0.15710144623763414 -0.18717168620634944 -0.15169355170344165 -0.16203101239337034 -0.16626913133593893 -0.156012286191294 -0.1917644486687281 -0.14489060157659955 -0.19706211600839882 -0.143690266540913 -0.15146055048573143 -0.16136280580833187 -0.1649481000003453 -0.23898174006592054 -0.16676400522661655 -0.1375380039098759 -0.16973567987398774 -0.2079913083143243 -0.19460155947238242 -0.18076649060415467 -0.13633613962234908 -0.21111972707959284 -0.13661638361912792 -0.17332233411512984 -0.1262455212732344 -0.15777467926072583 -0.12339499509814339 -0.3279727081381566 -0.17732292980637554 -0.15853653079541014 -0.1706515161458443 -0.1741310723945889 -0.1717769303222163 -0.1664413577835475 -0.17504821707160229 -0.15640276321663865 -0.1913974379291615 -0.13425798768490313 -0.16254591875218663 -0.2331440704534227 -0.15262421866780443 -0.20101097775273766 -0.15128663198517384 -0.16015712032852525 -0.19620190495663725 -0.13810609329680415 -0.49184791595426913 -0.281869137427643 -0.2261398392448608 -0.16555176465500973 -0.17423973151896077 -0.20334873471038636 -0.22706435970965047 -0.17105808533533276 -0.12307856091556256 -0.18149793956863022 -0.18622472706859186 -0.21902730735348763 -0.16376108822526292 -0.19903686962311998 -0.14200218984836366 -0.15521806871709803 -0.13524259692407592 -0.16684503358743258 -0.19242392318772025 -0.19340871316077074 -0.14490491807336284 -0.37157083536810864 -0.1872508829289553 -0.17267150407609813 -0.18382043158880687 -0.1896702088669725 -0.1831300198304076 -0.14823471056438312 -0.19597057242365426 -0.17507334244223902 -0.15562604743959338 -0.23113524042699798 -0.14251779841777437 -0.24030522887641634 -0.16528481882832646 -0.2106518492444197 -0.11796068983032708 -0.15694777207341268 -0.14717911829510635 -0.1583490037689314 -0.2017962722833632 -0.16968228584349143 -0.20921647132179433 -0.158078563753633 -0.13934345808618948 -0.19072919358809937 -0.2797255379119976 -0.1801353579372509 -0.22190751926020402 -0.14713852549632486 -0.15713625298006845 -0.16708830372125608 -0.24967315321464945 -0.23372418998246555 -0.19253561789396156 -0.13536377093604784 -0.16195857491915944 -0.16762976120750245 -0.1494367161795392 -0.19977361784148093 -0.1625385656930396 -0.17774025065846497 -0.14066970444865687 -0.14809968188043485 -0.25357132283462147 -0.1287256726414124 -0.14379860202271685 -0.16133655332179228 -0.17510325086388973 -0.21562809491438756 -0.19088981364394136 -0.15058359933969898 -0.11446561751502053 -0.24090351957412182 -0.14181990023153104 -0.1987265155842339 -0.1431506151731622 -0.17298127861998627 -0.15226319968698393 -0.12397893359721149 -0.18478365303437366 -0.17547764761285073 -0.1534833927850942 -0.13259329050946878 -0.16664422435562246 -0.1735845099523624 -0.19106786509854817 -0.21272999454862487 -0.15326846483160508 -0.3255894001555361 -0.22932088307962156 +0.35676082648741175 +0.34402859005051317 +0.3470647885008761 +0.404464047463586 +0.35673302506773813 +0.28819109468380133 +0.2768214842534659 +0.3218643171948218 +0.4566132252978298 +0.34157224618667303 +0.8502589001099329 +0.4037841365683954 +0.3970514119661808 +0.4050291550657542 +0.538959929522929 +0.3680256355553797 +0.4136036913002147 +0.35355656254854007 +0.417033125743629 +0.5437461540813695 +0.3391853613789528 +0.3436576302845641 +0.3410974487522541 +0.32044325331915396 +0.3847855267195515 +0.3954725677222862 +0.4953617663689878 +0.5293913477072131 +0.3359441657159409 +0.41096958399195166 +0.3003456693770497 +0.31821982450184005 +0.32751119949842367 +0.3311164031538617 +0.4111851522061698 +0.3187210967825235 +0.31466552053247376 +0.3745349907731219 +0.35456121832537324 +0.34527824983333666 +0.30568012639332565 +0.35106466542407455 +0.2918829371798508 +0.4087026734557547 +0.43783671003967223 +0.4242013452705209 +0.3567821916014614 +0.29620463553269566 +0.35486528747922036 +0.40032206424476335 +0.40987741313587356 +0.49193253332154846 +0.3552084515190098 +0.34438273668400343 +0.39428564809598377 +0.30812991584767657 +0.4378304720583256 +0.325367247236691 +0.36585549807398976 +0.30968204514359937 +0.6391334929226637 +0.30801711176163743 +0.31246363259144044 +0.32193701245845147 +0.4191880371486062 +0.27504816822700767 +0.3088269262093584 +0.3799598873900701 +0.27526309738241816 +0.3345403430222332 +0.3054056357833949 +0.3550361630221116 +0.3997273634253811 +0.46031584942439246 +0.40628874774638196 +0.29605966015768564 +0.35580746946027597 +0.3909936246241103 +0.3600356948987248 +1.003447612661871 +0.5448200362033521 +0.4487633650164724 +0.38569477300316724 +0.3751151883236858 +0.40359589021281606 +0.3723873657574889 +0.2928966778728621 +0.35615462500873946 +0.4205334464582104 +0.4020700838199034 +0.3619025397607522 +0.34384118959570004 +0.38945076828267483 +0.3210971973367387 +0.3915215733775214 +0.3038608919358574 +0.35593459250897286 +0.38867003362936753 +0.36421168828476763 +0.30685781220158975 +0.6452793865930938 +0.33357333854743587 +0.32329243364263344 +0.4017456510726739 +0.3861266315590922 +0.3247519896949844 +0.2956805565269558 +0.40925540212850203 +0.400778343711791 +0.3531636446508765 +0.3816728837227612 +0.4697388445092258 +0.48905669025936155 +0.3574598215874083 +0.38501457274889633 +0.29457343514471507 +0.34406000532038894 +0.23974374248072616 +0.3621724595640263 +0.4151102336101641 +0.3115355509602344 +0.3199729023054563 +0.4775746669171998 +0.34904691333933996 +0.35615198487135113 +0.4713550691419516 +0.32302540400402735 +0.3799585969885941 +0.3864166580665233 +0.2925324664825991 +0.4266296048807575 +0.554965752590992 +0.43342667300469223 +0.4189919754400696 +0.37177727614934347 +0.2655273120830455 +0.348733473929505 +0.33349648657491243 +0.3368164905302528 +0.343697192814395 +0.37853417968162456 +0.3499336722235412 +0.267099305633804 +0.45633115889514014 +0.33864943478745224 +0.4073825760662966 +0.34616725711867247 +0.39836532740628827 +0.43763453594094875 +0.290547608395029 +0.33623313911479347 +0.2926574817880619 +0.45834923284415485 +0.37157886569999166 +0.4060164144072639 +0.3407431814127573 +0.3309776469248096 +0.40963457117902596 +0.3052492016232938 +0.3127583254631216 +0.42505881440779614 +0.32243617098315414 +0.32509974113587703 +0.3672111799944095 +0.28228502081883744 +0.4376204997686252 +0.42962384412595517 +0.2946300879024689 +0.7478480214622951 +0.39331656941159554 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-calls/SAMPLE_0/std_psi_s_log__.tsv b/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-calls/SAMPLE_0/std_psi_s_log__.tsv index 52276844e0a..0a3c37391d5 100644 --- a/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-calls/SAMPLE_0/std_psi_s_log__.tsv +++ b/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-calls/SAMPLE_0/std_psi_s_log__.tsv @@ -2,4 +2,4 @@ @CO dtype:float64 @RG ID:GATKCopyNumber SM:SAMPLE_000 VALUE_0 -0.2685977912246379 +0.13269916055190087 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-calls/SAMPLE_0/std_read_depth_s_log__.tsv b/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-calls/SAMPLE_0/std_read_depth_s_log__.tsv index eb3f407859a..609a876003f 100644 --- a/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-calls/SAMPLE_0/std_read_depth_s_log__.tsv +++ b/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-calls/SAMPLE_0/std_read_depth_s_log__.tsv @@ -2,4 +2,4 @@ @CO dtype:float64 @RG ID:GATKCopyNumber SM:SAMPLE_000 VALUE_0 -0.004938883942509213 +0.00886525733916229 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-calls/SAMPLE_0/std_z_su.tsv b/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-calls/SAMPLE_0/std_z_su.tsv index 8b16ed954e0..9adbd00547b 100644 --- a/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-calls/SAMPLE_0/std_z_su.tsv +++ b/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-calls/SAMPLE_0/std_z_su.tsv @@ -1,9 +1,10 @@ -@CO shape:(5,) +@CO shape:(6,) @CO dtype:float64 @RG ID:GATKCopyNumber SM:SAMPLE_000 VALUE_0 -0.0060198679266026305 -0.008686644301693339 -0.009556215819076029 -0.007804009902181098 -0.011399608522621429 +0.08666609905783836 +0.019104038538349806 +0.019352207566272466 +0.024772482294391822 +0.0199147773041517 +0.029881461734426608 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-calls/calling_config.json b/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-calls/calling_config.json index 221a5e59350..e5d35d06a46 100644 --- a/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-calls/calling_config.json +++ b/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-calls/calling_config.json @@ -5,6 +5,6 @@ "num_calling_processes": 1, "num_copy_number_classes": 2, "num_copy_number_states": 6, - "p_active": 0.01, - "p_alt": 1e-06 + "p_active": 0.1, + "p_alt": 0.0005 } diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-calls/denoising_config.json b/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-calls/denoising_config.json index ae88afaa360..665b2dda813 100644 --- a/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-calls/denoising_config.json +++ b/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-calls/denoising_config.json @@ -8,10 +8,10 @@ "init_ard_rel_unexplained_variance": 0.1, "log_mean_bias_std": 0.1, "mapping_error_rate": 0.01, - "max_bias_factors": 5, + "max_bias_factors": 6, "num_gc_bins": 20, "num_samples_copy_ratio_approx": 200, - "psi_s_scale": 0.0001, - "psi_t_scale": 0.001, + "psi_s_scale": 0.01, + "psi_t_scale": 0.01, "q_c_expectation_mode": "hybrid" } diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-model/calling_config.json b/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-model/calling_config.json index 221a5e59350..e5d35d06a46 100644 --- a/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-model/calling_config.json +++ b/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-model/calling_config.json @@ -5,6 +5,6 @@ "num_calling_processes": 1, "num_copy_number_classes": 2, "num_copy_number_states": 6, - "p_active": 0.01, - "p_alt": 1e-06 + "p_active": 0.1, + "p_alt": 0.0005 } diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-model/denoising_config.json b/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-model/denoising_config.json index ae88afaa360..665b2dda813 100644 --- a/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-model/denoising_config.json +++ b/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-model/denoising_config.json @@ -8,10 +8,10 @@ "init_ard_rel_unexplained_variance": 0.1, "log_mean_bias_std": 0.1, "mapping_error_rate": 0.01, - "max_bias_factors": 5, + "max_bias_factors": 6, "num_gc_bins": 20, "num_samples_copy_ratio_approx": 200, - "psi_s_scale": 0.0001, - "psi_t_scale": 0.001, + "psi_s_scale": 0.01, + "psi_t_scale": 0.01, "q_c_expectation_mode": "hybrid" } diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-model/log_q_tau_tk.tsv b/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-model/log_q_tau_tk.tsv index 44b1d27d3df..92faf78e653 100644 --- a/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-model/log_q_tau_tk.tsv +++ b/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-model/log_q_tau_tk.tsv @@ -1,173 +1,173 @@ @CO shape:(170, 2) @CO dtype:float64 VALUE_0 VALUE_1 --3.725281194633112e-11 -24.013291167496703 --3.725281194633112e-11 -24.013291167497243 --3.725281194633112e-11 -24.013291167491882 --3.725281194633112e-11 -24.013291223062915 --5.4162530343682125e-05 -9.823548291974252 --6.545911561128825e-07 -14.23925533251063 --7.68737912515971e-05 -9.473383992015583 --5.419183219390611e-07 -14.428150835849781 --1.9064052199646575e-06 -13.170292115645939 --3.265941680435924e-05 -10.329393656753417 --9.467836538823438e-06 -11.567614862710018 --1.6414296276467955e-05 -11.017366086351187 --2.5482250398944917e-05 -10.577541152525166 --3.3435810938120536e-05 -10.305899766578355 --4.21897412972716e-05 -10.073354558132209 --6.012525330240104e-05 -9.719110678983753 --0.00010133625052893835 -9.197117025450641 --0.0002528652944324139 -8.282780074073305 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a/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-model/mu_W_tu.tsv b/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-model/mu_W_tu.tsv index f91971dac26..e00baf31de2 100644 --- a/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-model/mu_W_tu.tsv +++ b/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-model/mu_W_tu.tsv @@ -1,173 +1,173 @@ -@CO shape:(170, 5) +@CO shape:(170, 6) @CO dtype:float64 -VALUE_0 VALUE_1 VALUE_2 VALUE_3 VALUE_4 -1.3455962192349402 -0.40547691342086734 0.40030617701337695 0.7654667794853783 -0.9716304040815038 -1.0760137372488798 1.3092606119343144 0.6095530625572468 -1.2418495237258314 0.14310855404673944 -0.22687020336126032 2.1948438013523788 0.8978050105082429 -1.7348841353777757 -0.27601875840621604 --1.6847051853120238 -0.8349717189989547 0.9452851304795972 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a/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-model/mu_ard_u_log__.tsv +++ b/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-model/mu_ard_u_log__.tsv @@ -1,8 +1,9 @@ -@CO shape:(5,) +@CO shape:(6,) @CO dtype:float64 VALUE_0 -0.12712028602248157 -0.47849204340084184 -0.49432339011794635 -0.6334384230537421 -1.2103392171785001 +3.3157452315872797 +0.27700210936024544 +0.17155080231183484 +0.5966390764523473 +0.332508299459193 +1.124462475245523 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-model/mu_log_mean_bias_t.tsv b/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-model/mu_log_mean_bias_t.tsv index 8645c77056b..1066841cfb5 100644 --- a/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-model/mu_log_mean_bias_t.tsv +++ 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a/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-model/mu_psi_t_log__.tsv +++ b/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/gcnv-numerical-accuracy/shard_0-model/mu_psi_t_log__.tsv @@ -1,173 +1,173 @@ @CO shape:(170,) @CO dtype:float64 VALUE_0 --7.083401974142652 --6.430622810466955 --6.638068421227351 --6.443532774915745 --7.574796167118957 --7.648937031516749 --7.351442211736393 --7.286953304383077 --4.941756260293991 --6.632201602588492 --6.143612748847018 --6.731553295552037 --6.523583895221511 --6.400128707025179 --6.991383486487037 --6.147435028741098 --7.335006666755276 --6.15933881317624 --5.834591093941761 --5.264712907403523 --6.335514954215225 --6.960985437619794 --7.040087354563206 --7.49060734131809 --6.411204716427909 --7.032170143219522 --5.469833949326803 --6.739152041603303 --6.433289461657926 --6.444513490087429 --7.591727179572105 --6.5406243942189555 --6.398500584751756 --6.402574280758564 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