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feat: Add variant types parameter for filtering
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@Rapsssito
Rapsssito committed Oct 30, 2023
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11 changes: 4 additions & 7 deletions example/input/callers_folder/variant_caller_1/aggregated_metrics.csv
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variant_type,variant_size,window_radius,recall,precision,f1_score,tp,fp,fn,protein_affected_genes_count,protein_affected_driver_genes_count,protein_affected_genes,protein_affected_driver_genes
SNV,1,0,1.0,0.3333333333333333,0.5,3,2,0,2,1,PRDM16;ZSWIM7,PRDM16
INDEL,1 - 100,0,0.5,0.6666666666666666,0.5714285714285715,3,2,3,0,0,,
INS / DUP,1 - 100,0,0.3333333333333333,1.0,0.5,1,0,2,0,0,,
INS/DUP,1 - 100,0,0.3333333333333333,1.0,0.5,1,0,2,0,0,,
DEL,1 - 100,0,0.6666666666666666,0.3333333333333333,0.4444444444444444,2,2,1,0,0,,
SV,ALL,100,0.0,0.0,0.0,0,0,12,0,0,,
SV,ALL,100,0.0,0.0,0.0,0,0,13,0,0,,
TRA,TRA,100,0.0,0.0,0.0,0,0,3,0,0,,
INV,> 0,100,0.0,0.0,0.0,0,0,3,0,0,,
INV,1 - 100,100,0.0,0.0,0.0,0,0,0,0,0,,
INV,101 - 500,100,0.0,0.0,0.0,0,0,0,0,0,,
INV,> 500,100,0.0,0.0,0.0,0,0,3,0,0,,
INS,> 100,100,0.0,0.0,0.0,0,0,0,0,0,,
INS,101 - 500,100,0.0,0.0,0.0,0,0,0,0,0,,
INS,> 500,100,0.0,0.0,0.0,0,0,0,0,0,,
DEL,> 100,100,0.0,0.0,0.0,0,0,3,0,0,,
DEL,> 100,100,0.0,0.0,0.0,0,0,4,0,0,,
DEL,101 - 500,100,0.0,0.0,0.0,0,0,0,0,0,,
DEL,> 500,100,0.0,0.0,0.0,0,0,3,0,0,,
DEL,> 500,100,0.0,0.0,0.0,0,0,4,0,0,,
DUP,> 100,100,0.0,0.0,0.0,0,0,3,0,0,,
DUP,101 - 500,100,0.0,0.0,0.0,0,0,0,0,0,,
DUP,> 500,100,0.0,0.0,0.0,0,0,3,0,0,,
4 changes: 2 additions & 2 deletions example/input/callers_folder/variant_caller_1/config.tsv
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sample_name sample_types reference_fasta_path truth_vcf_paths test_vcf_paths
sample_2 precision ./fake_ref.fa ./input/truth/sample_2/truth_sample_2.vcf ./output/combinations/variant_caller_1/sample_2/*.vcf.gz,./output/combinations/variant_caller_1/sample_2/*.vcf,./output/combinations/variant_caller_1/sample_2/*.bcf
sample_1 recall ./fake_ref.fa ./input/truth/sample_1/truth_sample_1.vcf ./output/combinations/variant_caller_1/sample_1/*.vcf.gz,./output/combinations/variant_caller_1/sample_1/*.vcf,./output/combinations/variant_caller_1/sample_1/*.bcf
sample_1 recall ./fake_ref.fa ./input/truth/sample_1/truth_sample_1.vcf ./input/test/variant_caller_1/sample_1/*.vcf.gz,./input/test/variant_caller_1/sample_1/*.vcf,./input/test/variant_caller_1/sample_1/*.bcf
sample_2 precision ./fake_ref.fa ./input/truth/sample_2/truth_sample_2.vcf ./input/test/variant_caller_1/sample_2/*.vcf.gz,./input/test/variant_caller_1/sample_2/*.vcf,./input/test/variant_caller_1/sample_2/*.bcf
11 changes: 11 additions & 0 deletions example/input/callers_folder/variant_caller_1/samples/sample_1/pipelinefn.indel.vcf
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##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##FILTER=<ID=FAIL,Description="Fail the site if all alleles fail but for different reasons.">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##contig=<ID=1,length=249250621>
##contig=<ID=2,length=243199373>
##vcf_ops=../../../modules/oncoliner_assesment/src/assesment_bulk.py -c ./output/evaluations/variant_caller_1/config.tsv -p 8 -o ./output/evaluations/variant_caller_1 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR
1 26 . CTTTA C . PASS INDEL GT 0/0 0/1
1 31 . C CAAAAA . PASS INDEL GT 0/0 0/1
1 34 . C CAAAAA . PASS INDEL GT 0/0 0/1
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21 changes: 21 additions & 0 deletions example/input/callers_folder/variant_caller_1/samples/sample_1/pipelinefn.sv.vcf
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##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##FILTER=<ID=FAIL,Description="Fail the site if all alleles fail but for different reasons.">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##contig=<ID=1,length=249250621>
##contig=<ID=2,length=243199373>
##vcf_ops=../../../modules/oncoliner_assesment/src/assesment_bulk.py -c ./output/evaluations/variant_caller_1/config.tsv -p 8 -o ./output/evaluations/variant_caller_1 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR
1 11100 . N N[1:12100[ . PASS DEL GT 0/0 0/1
1 11100 . N N[1:13100[ . PASS DEL GT 0/0 0/1
1 11100 . N N[1:14100[ . PASS DEL GT 0/0 0/1
1 11100 . N N[1:15100[ . PASS DEL GT 0/0 0/1
1 21100 . N ]1:22100]N . PASS DUP GT 0/0 0/1
1 21100 . N ]1:23100]N . PASS DUP GT 0/0 0/1
1 21100 . N ]1:24100]N . PASS DUP GT 0/0 0/1
1 31100 . N [1:32100[N . PASS INV GT 0/0 0/1
1 31100 . N [1:33100[N . PASS INV GT 0/0 0/1
1 31100 . N [1:34100[N . PASS INV GT 0/0 0/1
1 41100 . N N[2:42100[ . PASS TRA GT 0/0 0/1
1 41100 . N [2:43100[N . PASS TRA GT 0/0 0/1
1 41100 . N N]2:44100] . PASS TRA GT 0/0 0/1
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9 changes: 9 additions & 0 deletions example/input/callers_folder/variant_caller_1/samples/sample_1/pipelinefp.indel.vcf
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##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##FILTER=<ID=FAIL,Description="Fail the site if all alleles fail but for different reasons.">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##contig=<ID=1,length=249250621>
##contig=<ID=2,length=243199373>
##vcf_ops=../../../modules/oncoliner_assesment/src/assesment_bulk.py -c ./output/evaluations/variant_caller_1/config.tsv -p 8 -o ./output/evaluations/variant_caller_1 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR
1 126 . CTTTA C . PASS FP;INDEL GT 0/0 0/1
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13 changes: 5 additions & 8 deletions example/input/callers_folder/variant_caller_1/samples/sample_1/pipelinemetrics.csv
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variant_type,variant_size,window_radius,recall,precision,f1_score,tp,fp,fn,protein_affected_genes_count,protein_affected_driver_genes_count,protein_affected_genes,protein_affected_driver_genes
SNV,1,0,1.0,1.0,1.0,3,0,0,2,1,ZSWIM7;PRDM16,PRDM16
SNV,1,0,1.0,1.0,1.0,3,0,0,2,1,PRDM16;ZSWIM7,PRDM16
INDEL,1 - 100,0,0.5,0.75,0.6,3,1,3,0,0,,
INS / DUP,1 - 100,0,0.3333333333333333,1.0,0.5,1,0,2,0,0,,
INS/DUP,1 - 100,0,0.3333333333333333,1.0,0.5,1,0,2,0,0,,
DEL,1 - 100,0,0.6666666666666666,0.6666666666666666,0.6666666666666666,2,1,1,0,0,,
SV,ALL,100,0.0,0.0,0.0,0,0,12,0,0,,
SV,ALL,100,0.0,0.0,0.0,0,0,13,0,0,,
TRA,TRA,100,0.0,0.0,0.0,0,0,3,0,0,,
INV,> 0,100,0.0,0.0,0.0,0,0,3,0,0,,
INV,1 - 100,100,0.0,0.0,0.0,0,0,0,0,0,,
INV,101 - 500,100,0.0,0.0,0.0,0,0,0,0,0,,
INV,> 500,100,0.0,0.0,0.0,0,0,3,0,0,,
INS,> 100,100,0.0,0.0,0.0,0,0,0,0,0,,
INS,101 - 500,100,0.0,0.0,0.0,0,0,0,0,0,,
INS,> 500,100,0.0,0.0,0.0,0,0,0,0,0,,
DEL,> 100,100,0.0,0.0,0.0,0,0,3,0,0,,
DEL,> 100,100,0.0,0.0,0.0,0,0,4,0,0,,
DEL,101 - 500,100,0.0,0.0,0.0,0,0,0,0,0,,
DEL,> 500,100,0.0,0.0,0.0,0,0,3,0,0,,
DEL,> 500,100,0.0,0.0,0.0,0,0,4,0,0,,
DUP,> 100,100,0.0,0.0,0.0,0,0,3,0,0,,
DUP,101 - 500,100,0.0,0.0,0.0,0,0,0,0,0,,
DUP,> 500,100,0.0,0.0,0.0,0,0,3,0,0,,
11 changes: 11 additions & 0 deletions example/input/callers_folder/variant_caller_1/samples/sample_1/pipelinetp.indel.vcf
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##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##FILTER=<ID=FAIL,Description="Fail the site if all alleles fail but for different reasons.">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##contig=<ID=1,length=249250621>
##contig=<ID=2,length=243199373>
##vcf_ops=../../../modules/oncoliner_assesment/src/assesment_bulk.py -c ./output/evaluations/variant_caller_1/config.tsv -p 8 -o ./output/evaluations/variant_caller_1 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR
1 20 . CTTTA C . PASS TP;INDEL GT 0/0 0/1
1 29 . CTTTA C . PASS TP;INDEL GT 0/0 0/1
1 37 . C CAAAAA . PASS TP;INDEL GT 0/0 0/1
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11 changes: 11 additions & 0 deletions example/input/callers_folder/variant_caller_1/samples/sample_1/pipelinetp.snv.vcf
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##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##FILTER=<ID=FAIL,Description="Fail the site if all alleles fail but for different reasons.">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##contig=<ID=1,length=249250621>
##contig=<ID=2,length=243199373>
##vcf_ops=../../../modules/oncoliner_assesment/src/assesment_bulk.py -c ./output/evaluations/variant_caller_1/config.tsv -p 8 -o ./output/evaluations/variant_caller_1 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR
1 10 . A C . PASS TP;SNV;CSQ=ENSG00000142611|ZSWIM7|protein_altering_variant,ENSG00000142611|PRDM16|protein_altering_variant GT 0/0 0/1
1 11 . A C . PASS TP;SNV GT 0/0 0/1
1 12 . A C . PASS TP;SNV GT 0/0 0/1
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10 changes: 10 additions & 0 deletions example/input/callers_folder/variant_caller_1/samples/sample_2/pipelinefn.indel.vcf
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##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##FILTER=<ID=FAIL,Description="Fail the site if all alleles fail but for different reasons.">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##contig=<ID=1,length=249250621>
##contig=<ID=2,length=243199373>
##vcf_ops=../../../modules/oncoliner_assesment/src/assesment_bulk.py -c ./output/evaluations/variant_caller_1/config.tsv -p 8 -o ./output/evaluations/variant_caller_1 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR
1 26 . CTTTA C . PASS INDEL GT 0/0 0/1
1 29 . CTTTA C . PASS INDEL GT 0/0 0/1
Binary file removed example/input/callers_folder/variant_caller_1/samples/sample_2/pipelinefn.indel.vcf.gz
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10 changes: 10 additions & 0 deletions example/input/callers_folder/variant_caller_1/samples/sample_2/pipelinefn.snv.vcf
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##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##FILTER=<ID=FAIL,Description="Fail the site if all alleles fail but for different reasons.">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##contig=<ID=1,length=249250621>
##contig=<ID=2,length=243199373>
##vcf_ops=../../../modules/oncoliner_assesment/src/assesment_bulk.py -c ./output/evaluations/variant_caller_1/config.tsv -p 8 -o ./output/evaluations/variant_caller_1 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR
1 11 . A C . PASS SNV GT 0/0 0/1
1 12 . A C . PASS SNV GT 0/0 0/1
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21 changes: 21 additions & 0 deletions example/input/callers_folder/variant_caller_1/samples/sample_2/pipelinefn.sv.vcf
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##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##FILTER=<ID=FAIL,Description="Fail the site if all alleles fail but for different reasons.">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##contig=<ID=1,length=249250621>
##contig=<ID=2,length=243199373>
##vcf_ops=../../../modules/oncoliner_assesment/src/assesment_bulk.py -c ./output/evaluations/variant_caller_1/config.tsv -p 8 -o ./output/evaluations/variant_caller_1 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR
1 11100 . N N[1:12100[ . PASS DEL GT 0/0 0/1
1 11100 . N N[1:13100[ . PASS DEL GT 0/0 0/1
1 11100 . N N[1:14100[ . PASS DEL GT 0/0 0/1
1 11100 . N N[1:15100[ . PASS DEL GT 0/0 0/1
1 21100 . N ]1:22100]N . PASS DUP GT 0/0 0/1
1 21100 . N ]1:23100]N . PASS DUP GT 0/0 0/1
1 21100 . N ]1:24100]N . PASS DUP GT 0/0 0/1
1 31100 . N [1:32100[N . PASS INV GT 0/0 0/1
1 31100 . N [1:33100[N . PASS INV GT 0/0 0/1
1 31100 . N [1:34100[N . PASS INV GT 0/0 0/1
1 41100 . N N[2:42100[ . PASS TRA GT 0/0 0/1
1 41100 . N [2:43100[N . PASS TRA GT 0/0 0/1
1 41100 . N N]2:44100] . PASS TRA GT 0/0 0/1
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10 changes: 10 additions & 0 deletions example/input/callers_folder/variant_caller_1/samples/sample_2/pipelinefp.indel.vcf
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##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##FILTER=<ID=FAIL,Description="Fail the site if all alleles fail but for different reasons.">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##contig=<ID=1,length=249250621>
##contig=<ID=2,length=243199373>
##vcf_ops=../../../modules/oncoliner_assesment/src/assesment_bulk.py -c ./output/evaluations/variant_caller_1/config.tsv -p 8 -o ./output/evaluations/variant_caller_1 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR
1 126 . CTTTA C . PASS FP;INDEL GT 0/0 0/1
1 129 . CTTTA C . PASS FP;INDEL GT 0/0 0/1
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10 changes: 10 additions & 0 deletions example/input/callers_folder/variant_caller_1/samples/sample_2/pipelinefp.snv.vcf
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##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##FILTER=<ID=FAIL,Description="Fail the site if all alleles fail but for different reasons.">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##contig=<ID=1,length=249250621>
##contig=<ID=2,length=243199373>
##vcf_ops=../../../modules/oncoliner_assesment/src/assesment_bulk.py -c ./output/evaluations/variant_caller_1/config.tsv -p 8 -o ./output/evaluations/variant_caller_1 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR
1 111 . A C . PASS FP;SNV GT 0/0 0/1
1 112 . A C . PASS FP;SNV GT 0/0 0/1
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13 changes: 5 additions & 8 deletions example/input/callers_folder/variant_caller_1/samples/sample_2/pipelinemetrics.csv
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@@ -1,20 +1,17 @@
variant_type,variant_size,window_radius,recall,precision,f1_score,tp,fp,fn,protein_affected_genes_count,protein_affected_driver_genes_count,protein_affected_genes,protein_affected_driver_genes
SNV,1,0,0.3333333333333333,0.3333333333333333,0.3333333333333333,1,2,2,2,1,ZSWIM7;PRDM16,PRDM16
SNV,1,0,0.3333333333333333,0.3333333333333333,0.3333333333333333,1,2,2,2,1,PRDM16;ZSWIM7,PRDM16
INDEL,1 - 100,0,0.6666666666666666,0.6666666666666666,0.6666666666666666,4,2,2,0,0,,
INS / DUP,1 - 100,0,1.0,1.0,1.0,3,0,0,0,0,,
INS/DUP,1 - 100,0,1.0,1.0,1.0,3,0,0,0,0,,
DEL,1 - 100,0,0.3333333333333333,0.3333333333333333,0.3333333333333333,1,2,2,0,0,,
SV,ALL,100,0.0,0.0,0.0,0,0,12,0,0,,
SV,ALL,100,0.0,0.0,0.0,0,0,13,0,0,,
TRA,TRA,100,0.0,0.0,0.0,0,0,3,0,0,,
INV,> 0,100,0.0,0.0,0.0,0,0,3,0,0,,
INV,1 - 100,100,0.0,0.0,0.0,0,0,0,0,0,,
INV,101 - 500,100,0.0,0.0,0.0,0,0,0,0,0,,
INV,> 500,100,0.0,0.0,0.0,0,0,3,0,0,,
INS,> 100,100,0.0,0.0,0.0,0,0,0,0,0,,
INS,101 - 500,100,0.0,0.0,0.0,0,0,0,0,0,,
INS,> 500,100,0.0,0.0,0.0,0,0,0,0,0,,
DEL,> 100,100,0.0,0.0,0.0,0,0,3,0,0,,
DEL,> 100,100,0.0,0.0,0.0,0,0,4,0,0,,
DEL,101 - 500,100,0.0,0.0,0.0,0,0,0,0,0,,
DEL,> 500,100,0.0,0.0,0.0,0,0,3,0,0,,
DEL,> 500,100,0.0,0.0,0.0,0,0,4,0,0,,
DUP,> 100,100,0.0,0.0,0.0,0,0,3,0,0,,
DUP,101 - 500,100,0.0,0.0,0.0,0,0,0,0,0,,
DUP,> 500,100,0.0,0.0,0.0,0,0,3,0,0,,
12 changes: 12 additions & 0 deletions example/input/callers_folder/variant_caller_1/samples/sample_2/pipelinetp.indel.vcf
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##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##FILTER=<ID=FAIL,Description="Fail the site if all alleles fail but for different reasons.">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##contig=<ID=1,length=249250621>
##contig=<ID=2,length=243199373>
##vcf_ops=../../../modules/oncoliner_assesment/src/assesment_bulk.py -c ./output/evaluations/variant_caller_1/config.tsv -p 8 -o ./output/evaluations/variant_caller_1 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR
1 20 . CTTTA C . PASS TP;INDEL GT 0/0 0/1
1 31 . C CAAAAA . PASS TP;INDEL GT 0/0 0/1
1 34 . C CAAAAA . PASS TP;INDEL GT 0/0 0/1
1 37 . C CAAAAA . PASS TP;INDEL GT 0/0 0/1
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9 changes: 9 additions & 0 deletions example/input/callers_folder/variant_caller_1/samples/sample_2/pipelinetp.snv.vcf
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##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##FILTER=<ID=FAIL,Description="Fail the site if all alleles fail but for different reasons.">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##contig=<ID=1,length=249250621>
##contig=<ID=2,length=243199373>
##vcf_ops=../../../modules/oncoliner_assesment/src/assesment_bulk.py -c ./output/evaluations/variant_caller_1/config.tsv -p 8 -o ./output/evaluations/variant_caller_1 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR
1 10 . A C . PASS TP;SNV;CSQ=ENSG00000142611|ZSWIM7|protein_altering_variant,ENSG00000142611|PRDM16|protein_altering_variant GT 0/0 0/1
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13 changes: 5 additions & 8 deletions example/input/callers_folder/variant_caller_2/aggregated_metrics.csv
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@@ -1,20 +1,17 @@
variant_type,variant_size,window_radius,recall,precision,f1_score,tp,fp,fn,protein_affected_genes_count,protein_affected_driver_genes_count,protein_affected_genes,protein_affected_driver_genes
SNV,1,0,0.3333333333333333,1.0,0.5,1,0,2,2,1,PRDM16;ZSWIM7,PRDM16
SNV,1,0,0.3333333333333333,1.0,0.5,1,0,2,2,1,ZSWIM7;PRDM16,PRDM16
INDEL,1 - 100,0,0.8333333333333334,0.75,0.7894736842105262,5,1,1,0,0,,
INS / DUP,1 - 100,0,1.0,1.0,1.0,3,0,0,0,0,,
INS/DUP,1 - 100,0,1.0,1.0,1.0,3,0,0,0,0,,
DEL,1 - 100,0,0.6666666666666666,0.0,0.0,2,1,1,0,0,,
SV,ALL,100,0.0,0.0,0.0,0,0,12,0,0,,
SV,ALL,100,0.0,0.0,0.0,0,0,13,0,0,,
TRA,TRA,100,0.0,0.0,0.0,0,0,3,0,0,,
INV,> 0,100,0.0,0.0,0.0,0,0,3,0,0,,
INV,1 - 100,100,0.0,0.0,0.0,0,0,0,0,0,,
INV,101 - 500,100,0.0,0.0,0.0,0,0,0,0,0,,
INV,> 500,100,0.0,0.0,0.0,0,0,3,0,0,,
INS,> 100,100,0.0,0.0,0.0,0,0,0,0,0,,
INS,101 - 500,100,0.0,0.0,0.0,0,0,0,0,0,,
INS,> 500,100,0.0,0.0,0.0,0,0,0,0,0,,
DEL,> 100,100,0.0,0.0,0.0,0,0,3,0,0,,
DEL,> 100,100,0.0,0.0,0.0,0,0,4,0,0,,
DEL,101 - 500,100,0.0,0.0,0.0,0,0,0,0,0,,
DEL,> 500,100,0.0,0.0,0.0,0,0,3,0,0,,
DEL,> 500,100,0.0,0.0,0.0,0,0,4,0,0,,
DUP,> 100,100,0.0,0.0,0.0,0,0,3,0,0,,
DUP,101 - 500,100,0.0,0.0,0.0,0,0,0,0,0,,
DUP,> 500,100,0.0,0.0,0.0,0,0,3,0,0,,
4 changes: 2 additions & 2 deletions example/input/callers_folder/variant_caller_2/config.tsv
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@@ -1,3 +1,3 @@
sample_name sample_types reference_fasta_path truth_vcf_paths test_vcf_paths
sample_2 precision ./fake_ref.fa ./input/truth/sample_2/truth_sample_2.vcf ./output/combinations/variant_caller_2/sample_2/*.vcf.gz,./output/combinations/variant_caller_2/sample_2/*.vcf,./output/combinations/variant_caller_2/sample_2/*.bcf
sample_1 recall ./fake_ref.fa ./input/truth/sample_1/truth_sample_1.vcf ./output/combinations/variant_caller_2/sample_1/*.vcf.gz,./output/combinations/variant_caller_2/sample_1/*.vcf,./output/combinations/variant_caller_2/sample_1/*.bcf
sample_1 recall ./fake_ref.fa ./input/truth/sample_1/truth_sample_1.vcf ./input/test/variant_caller_2/sample_1/*.vcf.gz,./input/test/variant_caller_2/sample_1/*.vcf,./input/test/variant_caller_2/sample_1/*.bcf
sample_2 precision ./fake_ref.fa ./input/truth/sample_2/truth_sample_2.vcf ./input/test/variant_caller_2/sample_2/*.vcf.gz,./input/test/variant_caller_2/sample_2/*.vcf,./input/test/variant_caller_2/sample_2/*.bcf
9 changes: 9 additions & 0 deletions example/input/callers_folder/variant_caller_2/samples/sample_1/pipelinefn.indel.vcf
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##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##FILTER=<ID=FAIL,Description="Fail the site if all alleles fail but for different reasons.">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##contig=<ID=1,length=249250621>
##contig=<ID=2,length=243199373>
##vcf_ops=../../../modules/oncoliner_assesment/src/assesment_bulk.py -c ./output/evaluations/variant_caller_2/config.tsv -p 8 -o ./output/evaluations/variant_caller_2 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR
1 26 . CTTTA C . PASS INDEL GT 0/0 0/1
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10 changes: 10 additions & 0 deletions example/input/callers_folder/variant_caller_2/samples/sample_1/pipelinefn.snv.vcf
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##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##FILTER=<ID=FAIL,Description="Fail the site if all alleles fail but for different reasons.">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##contig=<ID=1,length=249250621>
##contig=<ID=2,length=243199373>
##vcf_ops=../../../modules/oncoliner_assesment/src/assesment_bulk.py -c ./output/evaluations/variant_caller_2/config.tsv -p 8 -o ./output/evaluations/variant_caller_2 -it 100 -wr 100 --sv-size-bins 500 --contigs 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y --variant-types SNV INDEL-INS INDEL-DUP INDEL-DEL SV-TRA SV-INV SV-DEL SV-DUP --no-gzip
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR
1 11 . A C . PASS SNV GT 0/0 0/1
1 12 . A C . PASS SNV GT 0/0 0/1
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