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fix: Fix assessment typo
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@Rapsssito
Rapsssito committed Dec 11, 2023
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14 changes: 7 additions & 7 deletions CHANGELOG.md
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Expand Up @@ -22,7 +22,7 @@ BREAKING CHANGE: Dummy to trigger 1.0.0 ([`de5cfc0`](https://github.com/EUCANCan

* feat(UI): Add default column ordering ([`6f792fc`](https://github.com/EUCANCan/oncoliner/commit/6f792fcf399af30013dc0b45e33dde87e88083cf))

* feat: Add fixed row with the baseline ([`3907eab`](https://github.com/EUCANCan/oncoliner/commit/3907eabed350d85ce2f30e8d30267f93b61af02e))
* feat: Add fixeassessmenth the baseline ([`3907eab`](https://github.com/EUCANCan/oncoliner/commit/3907eabed350d85ce2f30e8d30267f93b61af02e))

* feat: Add variant callers combinations ([`4fbc459`](https://github.com/EUCANCan/oncoliner/commit/4fbc4595b2de0390fc9600db6d162a29c74469e2))

Expand Down Expand Up @@ -68,12 +68,12 @@ Co-authored-by: Henri de Soyres <[email protected]> ([`23cea50`](ht

* fix(UI): Remove lateral panels in improvement and harmonization (#2)

* removed left panel for improvement and harmonization views, changed into tab and new component: dropdown tree

* replaced variant type and size dropdown menu from list to accordion tree

---------

* removed left panel for improvement and harmonization views, changed into tab and new component: dropdown tree

* replaced variant type and size dropdown menu from list to accordion tree

---------

Co-authored-by: Henri de Soyres <[email protected]> ([`a2bc9f9`](https://github.com/EUCANCan/oncoliner/commit/a2bc9f9afe454ce1074f62f6cdf935d7c158bc74))

* fix(UI): Improve FP visibility in assesment ([`9b5c62b`](https://github.com/EUCANCan/oncoliner/commit/9b5c62ba9a1695330617b5a9e827551a74caf244))
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6 changes: 3 additions & 3 deletions README.md
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Expand Up @@ -208,11 +208,11 @@ A standalone tool that allows users to merge two different groups of VCF files.

## Modules

ONCOLINER is divided into three functional modules (assesment, improvement and harmonization) and a UI module. For more information about each module, check the corresponding README file in the [`modules`](/modules) folder:
ONCOLINER is divided into three functional modules (assessment, improvement and harmonization) and a UI module. For more information about each module, check the corresponding README file in the [`modules`](/modules) folder:

* [Assesment README](/modules/oncoliner_assesment/README.md)
* [Assessment README](/modules/oncoliner_assessment/README.md)
* [Improvement README](/modules/oncoliner_improvement/README.md)
* [Harmonization README](/modules/oncoliner_harmonization/README.md)
* [UI README](/modules/oncoliner_ui/README.md)

Each module can be run independently. However, the results of the assesment module are required to run the improvement module and the results of the improvement module are required to run the harmonization module. The UI module generates a report for the results of each module.
Each module can be run independently. However, the results of the assessment module are required to run the improvement module and the results of the improvement module are required to run the harmonization module. The UI module generates a report for the results of each module.
2 changes: 1 addition & 1 deletion example/example.sh
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@@ -1,5 +1,5 @@
export UI_COMMAND="python3 ../modules/oncoliner_ui/src/ui_main.py"
export ASSESMENT_COMMAND="python3 ../modules/oncoliner_assesment/src/assesment_bulk.py"
export ASSESSMENT_COMMAND="python3 ../modules/oncoliner_assessment/src/assessment_bulk.py"
export IMPROVEMENT_COMMAND="python3 ../modules/oncoliner_improvement/src/improvement_main.py"
export HARMONIZATION_COMMAND="python3 ../modules/oncoliner_harmonization/src/harmonization_main.py"

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2 changes: 1 addition & 1 deletion example/input/callers_folder/variant_caller_1/samples/sample_1/pipelinefn.indel.vcf
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Expand Up @@ -4,7 +4,7 @@
##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 1 -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
##vcf_ops=../../../modules/oncoliner_assessment/src/assessment_bulk.py -c ./output/evaluations/variant_caller_1/config.tsv -p 1 -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
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2 changes: 1 addition & 1 deletion example/input/callers_folder/variant_caller_1/samples/sample_1/pipelinefn.sv.vcf
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Expand Up @@ -4,7 +4,7 @@
##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 1 -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
##vcf_ops=../../../modules/oncoliner_assessment/src/assessment_bulk.py -c ./output/evaluations/variant_caller_1/config.tsv -p 1 -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
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2 changes: 1 addition & 1 deletion example/input/callers_folder/variant_caller_1/samples/sample_1/pipelinefp.indel.vcf
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Expand Up @@ -4,6 +4,6 @@
##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 1 -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
##vcf_ops=../../../modules/oncoliner_assessment/src/assessment_bulk.py -c ./output/evaluations/variant_caller_1/config.tsv -p 1 -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
2 changes: 1 addition & 1 deletion example/input/callers_folder/variant_caller_1/samples/sample_1/pipelinetp.indel.vcf
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Expand Up @@ -4,7 +4,7 @@
##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 1 -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
##vcf_ops=../../../modules/oncoliner_assessment/src/assessment_bulk.py -c ./output/evaluations/variant_caller_1/config.tsv -p 1 -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
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2 changes: 1 addition & 1 deletion example/input/callers_folder/variant_caller_1/samples/sample_1/pipelinetp.snv.vcf
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Expand Up @@ -4,7 +4,7 @@
##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 1 -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
##vcf_ops=../../../modules/oncoliner_assessment/src/assessment_bulk.py -c ./output/evaluations/variant_caller_1/config.tsv -p 1 -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
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2 changes: 1 addition & 1 deletion example/input/callers_folder/variant_caller_1/samples/sample_2/pipelinefn.indel.vcf
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Expand Up @@ -4,7 +4,7 @@
##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 1 -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
##vcf_ops=../../../modules/oncoliner_assessment/src/assessment_bulk.py -c ./output/evaluations/variant_caller_1/config.tsv -p 1 -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
2 changes: 1 addition & 1 deletion example/input/callers_folder/variant_caller_1/samples/sample_2/pipelinefn.snv.vcf
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Expand Up @@ -4,7 +4,7 @@
##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 1 -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
##vcf_ops=../../../modules/oncoliner_assessment/src/assessment_bulk.py -c ./output/evaluations/variant_caller_1/config.tsv -p 1 -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;ONCOLINER_PROT_GENES=TARBP1 GT 0/0 0/1
2 changes: 1 addition & 1 deletion example/input/callers_folder/variant_caller_1/samples/sample_2/pipelinefn.sv.vcf
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Expand Up @@ -4,7 +4,7 @@
##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 1 -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
##vcf_ops=../../../modules/oncoliner_assessment/src/assessment_bulk.py -c ./output/evaluations/variant_caller_1/config.tsv -p 1 -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
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2 changes: 1 addition & 1 deletion example/input/callers_folder/variant_caller_1/samples/sample_2/pipelinefp.indel.vcf
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Expand Up @@ -4,7 +4,7 @@
##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 1 -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
##vcf_ops=../../../modules/oncoliner_assessment/src/assessment_bulk.py -c ./output/evaluations/variant_caller_1/config.tsv -p 1 -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
2 changes: 1 addition & 1 deletion example/input/callers_folder/variant_caller_1/samples/sample_2/pipelinefp.snv.vcf
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Expand Up @@ -4,7 +4,7 @@
##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 1 -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
##vcf_ops=../../../modules/oncoliner_assessment/src/assessment_bulk.py -c ./output/evaluations/variant_caller_1/config.tsv -p 1 -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
2 changes: 1 addition & 1 deletion example/input/callers_folder/variant_caller_1/samples/sample_2/pipelinetp.indel.vcf
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Expand Up @@ -4,7 +4,7 @@
##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 1 -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
##vcf_ops=../../../modules/oncoliner_assessment/src/assessment_bulk.py -c ./output/evaluations/variant_caller_1/config.tsv -p 1 -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
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2 changes: 1 addition & 1 deletion example/input/callers_folder/variant_caller_1/samples/sample_2/pipelinetp.snv.vcf
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Expand Up @@ -4,6 +4,6 @@
##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 1 -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
##vcf_ops=../../../modules/oncoliner_assessment/src/assessment_bulk.py -c ./output/evaluations/variant_caller_1/config.tsv -p 1 -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
2 changes: 1 addition & 1 deletion example/input/callers_folder/variant_caller_2/samples/sample_1/pipelinefn.indel.vcf
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Expand Up @@ -4,6 +4,6 @@
##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 1 -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
##vcf_ops=../../../modules/oncoliner_assessment/src/assessment_bulk.py -c ./output/evaluations/variant_caller_2/config.tsv -p 1 -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
2 changes: 1 addition & 1 deletion example/input/callers_folder/variant_caller_2/samples/sample_1/pipelinefn.snv.vcf
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Expand Up @@ -4,7 +4,7 @@
##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 1 -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
##vcf_ops=../../../modules/oncoliner_assessment/src/assessment_bulk.py -c ./output/evaluations/variant_caller_2/config.tsv -p 1 -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;ONCOLINER_PROT_GENES=TARBP1 GT 0/0 0/1
2 changes: 1 addition & 1 deletion example/input/callers_folder/variant_caller_2/samples/sample_1/pipelinefn.sv.vcf
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##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 1 -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
##vcf_ops=../../../modules/oncoliner_assessment/src/assessment_bulk.py -c ./output/evaluations/variant_caller_2/config.tsv -p 1 -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 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
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2 changes: 1 addition & 1 deletion example/input/callers_folder/variant_caller_2/samples/sample_1/pipelinefp.snv.vcf
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##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 1 -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
##vcf_ops=../../../modules/oncoliner_assessment/src/assessment_bulk.py -c ./output/evaluations/variant_caller_2/config.tsv -p 1 -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
1 112 . A C . PASS FP;SNV GT 0/0 0/1
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