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provenance.ttl
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@base <http://snakemake-provenance> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix foaf: <http://xmlns.com/foaf/0.1/> .
@prefix sioc: <http://rdfs.org/sioc/ns#> .
@prefix prov: <http://www.w3.org/ns/prov#> .
@prefix sym: <http://fr.symetric/vocab#> .
@prefix crypto: <http://id.loc.gov/vocabulary/preservation/cryptographicHashFunctions#> .
@prefix dcterms: <http://purl.org/dc/terms/> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
<:gaignard-a> a prov:Agent, prov:Person .
<>
a prov:Bundle, prov:Entity;
prov:wasAttributedTo <:gaignard-a>;
prov:generatedAtTime "2019-01-23T15:27:59.432330"^^xsd:dateTime.
<http://snakemake-provenance#activity-b4d8e563-f04c-47cf-b2a6-b979d47c11ce>
a prov:Activity ;
rdfs:comment """
gunzip -k ../testdata/human_g1k_v37.chr22.fasta.gz
""" ;
prov:wasAssociatedWith <#unzipGenome> ;
prov:startedAtTime "2019-01-23T15:27:59.653033"^^xsd:dateTime;
prov:endedAtTime "2019-01-23T15:27:59.653041"^^xsd:dateTime;
prov:used <../testdata/human_g1k_v37.chr22.fasta.gz> ;
.
<../testdata/human_g1k_v37.chr22.fasta>
a prov:Entity;
prov:wasGeneratedBy <http://snakemake-provenance#activity-b4d8e563-f04c-47cf-b2a6-b979d47c11ce>;
prov:wasAssociatedWith <#unzipGenome> ;
rdfs:label "../testdata/human_g1k_v37.chr22.fasta";
prov:wasDerivedFrom <../testdata/human_g1k_v37.chr22.fasta.gz> ;
.
<http://snakemake-provenance#activity-78d70234-8fd0-47c0-aa23-4144f66c7b10>
a prov:Activity ;
prov:wasAssociatedWith <#downloadGATK> ;
prov:startedAtTime "2019-01-23T15:27:59.654284"^^xsd:dateTime;
prov:endedAtTime "2019-01-23T15:27:59.654294"^^xsd:dateTime;
.
<gatkPresent.txt>
a prov:Entity;
prov:wasGeneratedBy <http://snakemake-provenance#activity-78d70234-8fd0-47c0-aa23-4144f66c7b10>;
prov:wasAssociatedWith <#downloadGATK> ;
rdfs:label "gatkPresent.txt";
.
<http://snakemake-provenance#activity-a79831dc-95d4-46c3-b2ae-3db862c56796>
a prov:Activity ;
rdfs:comment """
samtools faidx ../testdata/human_g1k_v37.chr22.fasta
""" ;
prov:wasAssociatedWith <#genomeIndex> ;
prov:startedAtTime "2019-01-23T15:27:59.656028"^^xsd:dateTime;
prov:endedAtTime "2019-01-23T15:27:59.656037"^^xsd:dateTime;
prov:used <../testdata/human_g1k_v37.chr22.fasta> ;
.
<../testdata/human_g1k_v37.chr22.fasta.fai>
a prov:Entity;
prov:wasGeneratedBy <http://snakemake-provenance#activity-a79831dc-95d4-46c3-b2ae-3db862c56796>;
prov:wasAssociatedWith <#genomeIndex> ;
rdfs:label "../testdata/human_g1k_v37.chr22.fasta.fai";
prov:wasDerivedFrom <../testdata/human_g1k_v37.chr22.fasta> ;
.
<http://snakemake-provenance#activity-098dcde3-e9da-4c38-bd49-a508fa4e82db>
a prov:Activity ;
rdfs:comment """
bwa index -a bwtsw ../testdata/human_g1k_v37.chr22.fasta
""" ;
prov:wasAssociatedWith <#bwaIndex> ;
prov:startedAtTime "2019-01-23T15:27:59.657741"^^xsd:dateTime;
prov:endedAtTime "2019-01-23T15:27:59.657752"^^xsd:dateTime;
prov:used <../testdata/human_g1k_v37.chr22.fasta> ;
.
<../testdata/human_g1k_v37.chr22.fasta.bwt>
a prov:Entity;
prov:wasGeneratedBy <http://snakemake-provenance#activity-098dcde3-e9da-4c38-bd49-a508fa4e82db>;
prov:wasAssociatedWith <#bwaIndex> ;
rdfs:label "../testdata/human_g1k_v37.chr22.fasta.bwt";
prov:wasDerivedFrom <../testdata/human_g1k_v37.chr22.fasta> ;
.
<http://snakemake-provenance#activity-fb9c7950-0b6d-4402-a9d4-1b7c31f1b290>
a prov:Activity ;
rdfs:comment """
picard CreateSequenceDictionary REFERENCE=../testdata/human_g1k_v37.chr22.fasta OUTPUT=../testdata/human_g1k_v37.chr22.dict
""" ;
prov:wasAssociatedWith <#genomeDictionary> ;
prov:startedAtTime "2019-01-23T15:27:59.659530"^^xsd:dateTime;
prov:endedAtTime "2019-01-23T15:27:59.659540"^^xsd:dateTime;
prov:used <../testdata/human_g1k_v37.chr22.fasta> ;
.
<../testdata/human_g1k_v37.chr22.dict>
a prov:Entity;
prov:wasGeneratedBy <http://snakemake-provenance#activity-fb9c7950-0b6d-4402-a9d4-1b7c31f1b290>;
prov:wasAssociatedWith <#genomeDictionary> ;
rdfs:label "../testdata/human_g1k_v37.chr22.dict";
prov:wasDerivedFrom <../testdata/human_g1k_v37.chr22.fasta> ;
.
<http://snakemake-provenance#activity-e5a4336a-3495-4821-9bd2-24d444b61637>
a prov:Activity ;
rdfs:comment """
bwa mem -t 1 -M -H '@CO\tProject:test Sample:Sample1 Date:2019-01-23 CWD:/Users/gaignard-a/Documents/Dev/exome-provenance/exome-pipeline/output Capture:{ name : captureName , description : exome capture test chr22 , path : ../testdata/Broad.human.exome.b37.chr22.bed}' -R '@RG\tID:Sample1\tLB:Sample1\tSM:Sample1\tPL:Illumina\tCN:CENTER' ../testdata/human_g1k_v37.chr22.fasta ../testdata/Sample1_ATGCCTAA_L001_R1_001.fastq.gz ../testdata/Sample1_ATGCCTAA_L001_R2_001.fastq.gz > Samples/Sample1/BAM/Sample1.p1.aligned.sam
""" ;
prov:wasAssociatedWith <https://bio.tools/bwa_cloudifb> ;
prov:startedAtTime "2019-01-23T15:27:59.661594"^^xsd:dateTime;
prov:endedAtTime "2019-01-23T15:27:59.661606"^^xsd:dateTime;
prov:used <../testdata/human_g1k_v37.chr22.fasta> ;
prov:used <../testdata/Sample1_ATGCCTAA_L001_R1_001.fastq.gz> ;
prov:used <../testdata/Sample1_ATGCCTAA_L001_R2_001.fastq.gz> ;
prov:used <../testdata/human_g1k_v37.chr22.fasta.bwt> ;
.
<Samples/Sample1/BAM/Sample1.p1.aligned.sam>
a prov:Entity;
prov:wasGeneratedBy <http://snakemake-provenance#activity-e5a4336a-3495-4821-9bd2-24d444b61637>;
prov:wasAssociatedWith <https://bio.tools/bwa_cloudifb> ;
rdfs:label "Samples/Sample1/BAM/Sample1.p1.aligned.sam";
prov:wasDerivedFrom <../testdata/human_g1k_v37.chr22.fasta> ;
prov:wasDerivedFrom <../testdata/Sample1_ATGCCTAA_L001_R1_001.fastq.gz> ;
prov:wasDerivedFrom <../testdata/Sample1_ATGCCTAA_L001_R2_001.fastq.gz> ;
prov:wasDerivedFrom <../testdata/human_g1k_v37.chr22.fasta.bwt> ;
.
<http://snakemake-provenance#activity-91c40a1e-45f0-47c2-a19d-3e6d47d993ed>
a prov:Activity ;
rdfs:comment """
tr -d '\r' < ../testdata/Broad.human.exome.b37.chr22.bed | grep -v '^browser' | grep -v '^track' | cut -f1,2,3 | sed 's/^chr//' | LC_ALL=C sort -t ' ' -k1,1 -k2,2n -k3,3n | bedtools merge | bedtools sort -faidx ../testdata/human_g1k_v37.chr22.fasta.fai > BED/capture.bed
""" ;
prov:wasAssociatedWith <https://bio.tools/bedtools_mergebedgraph-ip> ;
prov:startedAtTime "2019-01-23T15:27:59.663524"^^xsd:dateTime;
prov:endedAtTime "2019-01-23T15:27:59.663534"^^xsd:dateTime;
prov:used <../testdata/Broad.human.exome.b37.chr22.bed> ;
prov:used <../testdata/human_g1k_v37.chr22.fasta.fai> ;
.
<BED/capture.bed>
a prov:Entity;
prov:wasGeneratedBy <http://snakemake-provenance#activity-91c40a1e-45f0-47c2-a19d-3e6d47d993ed>;
prov:wasAssociatedWith <https://bio.tools/bedtools_mergebedgraph-ip> ;
rdfs:label "BED/capture.bed";
prov:wasDerivedFrom <../testdata/Broad.human.exome.b37.chr22.bed> ;
prov:wasDerivedFrom <../testdata/human_g1k_v37.chr22.fasta.fai> ;
.
<http://snakemake-provenance#activity-b4de3b83-1cc6-4f48-ad48-540d300cf703>
a prov:Activity ;
rdfs:comment """
samtools sort --reference ../testdata/human_g1k_v37.chr22.fasta -l 9 -@ 1 -O bam -o Samples/Sample1/BAM/Sample1.p1.sorted.bam -T Samples/Sample1/BAM/Sample1.p1.sorted.bam.tmp Samples/Sample1/BAM/Sample1.p1.aligned.sam
""" ;
prov:wasAssociatedWith <https://bio.tools/samtools_sort-ip> ;
prov:startedAtTime "2019-01-23T15:27:59.665147"^^xsd:dateTime;
prov:endedAtTime "2019-01-23T15:27:59.665156"^^xsd:dateTime;
prov:used <../testdata/human_g1k_v37.chr22.fasta> ;
prov:used <../testdata/human_g1k_v37.chr22.fasta.fai> ;
prov:used <Samples/Sample1/BAM/Sample1.p1.aligned.sam> ;
.
<Samples/Sample1/BAM/Sample1.p1.sorted.bam>
a prov:Entity;
prov:wasGeneratedBy <http://snakemake-provenance#activity-b4de3b83-1cc6-4f48-ad48-540d300cf703>;
prov:wasAssociatedWith <https://bio.tools/samtools_sort-ip> ;
rdfs:label "Samples/Sample1/BAM/Sample1.p1.sorted.bam";
prov:wasDerivedFrom <../testdata/human_g1k_v37.chr22.fasta> ;
prov:wasDerivedFrom <../testdata/human_g1k_v37.chr22.fasta.fai> ;
prov:wasDerivedFrom <Samples/Sample1/BAM/Sample1.p1.aligned.sam> ;
.
<http://snakemake-provenance#activity-133b295b-41ad-40d1-be31-3d9f1821e220>
a prov:Activity ;
rdfs:comment """
bedtools slop -b 1000 -g ../testdata/human_g1k_v37.chr22.fasta.fai -i BED/capture.bed | LC_ALL=C sort -t ' ' -k1,1 -k2,2n -k3,3n | bedtools merge -d 1000 | bedtools sort -faidx ../testdata/human_g1k_v37.chr22.fasta.fai > BED/capture.extended1000.bed
""" ;
prov:wasAssociatedWith <https://bio.tools/bedtools_mergebedgraph-ip> ;
prov:startedAtTime "2019-01-23T15:27:59.666734"^^xsd:dateTime;
prov:endedAtTime "2019-01-23T15:27:59.666747"^^xsd:dateTime;
prov:used <BED/capture.bed> ;
prov:used <../testdata/human_g1k_v37.chr22.fasta.fai> ;
.
<BED/capture.extended1000.bed>
a prov:Entity;
prov:wasGeneratedBy <http://snakemake-provenance#activity-133b295b-41ad-40d1-be31-3d9f1821e220>;
prov:wasAssociatedWith <https://bio.tools/bedtools_mergebedgraph-ip> ;
rdfs:label "BED/capture.extended1000.bed";
prov:wasDerivedFrom <BED/capture.bed> ;
prov:wasDerivedFrom <../testdata/human_g1k_v37.chr22.fasta.fai> ;
.
<http://snakemake-provenance#activity-1df41f0b-a86f-41eb-95cf-cd41c2cb9a85>
a prov:Activity ;
prov:wasAssociatedWith <https://bio.tools/picard_tools> ;
prov:startedAtTime "2019-01-23T15:27:59.668077"^^xsd:dateTime;
prov:endedAtTime "2019-01-23T15:27:59.668091"^^xsd:dateTime;
prov:used <Samples/Sample1/BAM/Sample1.p1.sorted.bam> ;
.
<Samples/Sample1/BAM/Sample1.merged.bam>
a prov:Entity;
prov:wasGeneratedBy <http://snakemake-provenance#activity-1df41f0b-a86f-41eb-95cf-cd41c2cb9a85>;
prov:wasAssociatedWith <https://bio.tools/picard_tools> ;
rdfs:label "Samples/Sample1/BAM/Sample1.merged.bam";
prov:wasDerivedFrom <Samples/Sample1/BAM/Sample1.p1.sorted.bam> ;
.
<Samples/Sample1/BAM/Sample1.merged.bai>
a prov:Entity;
prov:wasGeneratedBy <http://snakemake-provenance#activity-1df41f0b-a86f-41eb-95cf-cd41c2cb9a85>;
prov:wasAssociatedWith <https://bio.tools/picard_tools> ;
rdfs:label "Samples/Sample1/BAM/Sample1.merged.bai";
prov:wasDerivedFrom <Samples/Sample1/BAM/Sample1.p1.sorted.bam> ;
.
<http://snakemake-provenance#activity-d41f5a7f-5523-487f-b092-8be4c1b7b42f>
a prov:Activity ;
rdfs:comment """
picard MarkDuplicates -Xmx5g TMP_DIR=Samples/Sample1/BAM MAX_RECORDS_IN_RAM=1000000 COMPRESSION_LEVEL=9 AS=true PG=PMD VALIDATION_STRINGENCY=SILENT CREATE_INDEX=true O=Samples/Sample1/BAM/Sample1.markdup.bam I=Samples/Sample1/BAM/Sample1.merged.bam M=Samples/Sample1/QC/Sample1.markdup.metrics
""" ;
prov:wasAssociatedWith <https://bio.tools/markduplicates_ip> ;
prov:startedAtTime "2019-01-23T15:27:59.670370"^^xsd:dateTime;
prov:endedAtTime "2019-01-23T15:27:59.670380"^^xsd:dateTime;
prov:used <Samples/Sample1/BAM/Sample1.merged.bam> ;
prov:used <Samples/Sample1/BAM/Sample1.merged.bai> ;
.
<Samples/Sample1/QC/Sample1.markdup.metrics>
a prov:Entity;
prov:wasGeneratedBy <http://snakemake-provenance#activity-d41f5a7f-5523-487f-b092-8be4c1b7b42f>;
prov:wasAssociatedWith <https://bio.tools/markduplicates_ip> ;
rdfs:label "Samples/Sample1/QC/Sample1.markdup.metrics";
prov:wasDerivedFrom <Samples/Sample1/BAM/Sample1.merged.bam> ;
prov:wasDerivedFrom <Samples/Sample1/BAM/Sample1.merged.bai> ;
.
<Samples/Sample1/BAM/Sample1.markdup.bam>
a prov:Entity;
prov:wasGeneratedBy <http://snakemake-provenance#activity-d41f5a7f-5523-487f-b092-8be4c1b7b42f>;
prov:wasAssociatedWith <https://bio.tools/markduplicates_ip> ;
rdfs:label "Samples/Sample1/BAM/Sample1.markdup.bam";
prov:wasDerivedFrom <Samples/Sample1/BAM/Sample1.merged.bam> ;
prov:wasDerivedFrom <Samples/Sample1/BAM/Sample1.merged.bai> ;
.
<Samples/Sample1/BAM/Sample1.markdup.bai>
a prov:Entity;
prov:wasGeneratedBy <http://snakemake-provenance#activity-d41f5a7f-5523-487f-b092-8be4c1b7b42f>;
prov:wasAssociatedWith <https://bio.tools/markduplicates_ip> ;
rdfs:label "Samples/Sample1/BAM/Sample1.markdup.bai";
prov:wasDerivedFrom <Samples/Sample1/BAM/Sample1.merged.bam> ;
prov:wasDerivedFrom <Samples/Sample1/BAM/Sample1.merged.bai> ;
.
<http://snakemake-provenance#activity-dde929a6-b8c0-42a7-a051-f02a370a07ab>
a prov:Activity ;
rdfs:comment """
gatk -Djava.io.tmpdir=Samples/Sample1/BAM -Xmx5g -T RealignerTargetCreator -nt 1 -R ../testdata/human_g1k_v37.chr22.fasta -L:capture,BED BED/capture.extended1000.bed -I Samples/Sample1/BAM/Sample1.markdup.bam -o Samples/Sample1/BAM/Sample1.realign.intervals --known:onekindels,VCF ../testdata/1000G_phase1.indels.b37.chr22.recode.vcf.gz --known:millsindels,VCF ../testdata/Mills_and_1000G_gold_standard.indels.b37.chr22.recode.vcf.gz -S SILENT
""" ;
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prov:wasDerivedFrom <../testdata/1000G_phase1.indels.b37.chr22.recode.vcf.gz> ;
prov:wasDerivedFrom <gatkPresent.txt> ;
prov:wasDerivedFrom <Samples/Sample1/BAM/Sample1.markdup.bai> ;
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a prov:Activity ;
rdfs:comment """
gatk -Djava.io.tmpdir=Samples/Sample1/BAM -XX:ParallelGCThreads=5 -Xmx2g -T IndelRealigner -R ../testdata/human_g1k_v37.chr22.fasta --bam_compression 9 -I Samples/Sample1/BAM/Sample1.markdup.bam -o Samples/Sample1/BAM/Sample1.realign.bam -targetIntervals Samples/Sample1/BAM/Sample1.realign.intervals -known:onekindels,VCF ../testdata/1000G_phase1.indels.b37.chr22.recode.vcf.gz -known:millsindels,VCF ../testdata/Mills_and_1000G_gold_standard.indels.b37.chr22.recode.vcf.gz -S SILENT
""" ;
prov:wasAssociatedWith <https://bio.tools/gatk2_indel_realigner-ip> ;
prov:startedAtTime "2019-01-23T15:27:59.674176"^^xsd:dateTime;
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prov:used <Samples/Sample1/BAM/Sample1.markdup.bai> ;
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prov:used <../testdata/Mills_and_1000G_gold_standard.indels.b37.chr22.recode.vcf.gz> ;
prov:used <../testdata/human_g1k_v37.chr22.dict> ;
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prov:wasDerivedFrom <../testdata/Mills_and_1000G_gold_standard.indels.b37.chr22.recode.vcf.gz> ;
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a prov:Activity ;
rdfs:comment """
gatk -Djava.io.tmpdir=Samples/Sample1/BAM -XX:ParallelGCThreads=5 -Xmx2g -T BaseRecalibrator -nct 1 -R ../testdata/human_g1k_v37.chr22.fasta --validation_strictness LENIENT -I Samples/Sample1/BAM/Sample1.realign.bam -l INFO -o Samples/Sample1/BAM/Sample1.recal.table -knownSites:dbsnp,VCF ../testdata/dbsnp_138.b37.chr22.recode.vcf.gz -L:capture,BED BED/capture.extended1000.bed -cov QualityScoreCovariate -cov CycleCovariate -cov ContextCovariate
""" ;
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a prov:Entity;
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a prov:Activity ;
rdfs:comment """
gatk -Djava.io.tmpdir=Samples/Sample1/BAM -XX:ParallelGCThreads=5 -Xmx4g -T PrintReads -nct 1 -R ../testdata/human_g1k_v37.chr22.fasta --bam_compression 9 -BQSR Samples/Sample1/BAM/Sample1.recal.table --disable_indel_quals -I Samples/Sample1/BAM/Sample1.realign.bam -o Samples/Sample1/BAM/Sample1.final.bam --validation_strictness LENIENT -l INFO
""" ;
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a prov:Activity ;
rdfs:comment """
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""" ;
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prov:used <gatkPresent.txt> ;
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a prov:Activity ;
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a prov:Activity ;
rdfs:comment """
gatk -Djava.io.tmpdir=VCF -XX:ParallelGCThreads=3 -Xmx10g -T CombineGVCFs -R ../testdata/human_g1k_v37.chr22.fasta --variant VCF/gvcf.list -S SILENT -o VCF/hapcaller.combined.g.vcf.gz
""" ;
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a prov:Activity ;
rdfs:comment """
gatk -Djava.io.tmpdir=VCF -XX:ParallelGCThreads=3 -Xmx3g -T GenotypeGVCFs -R ../testdata/human_g1k_v37.chr22.fasta --variant VCF/hapcaller.combined.g.vcf.gz -S SILENT -o VCF/hapcaller.genotyped.vcf.gz
""" ;
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a prov:Activity ;
rdfs:comment """
gatk -Djava.io.tmpdir=VCF -XX:ParallelGCThreads=3 -Xmx3g -T SelectVariants -R ../testdata/human_g1k_v37.chr22.fasta --logging_level FATAL -selectType INDEL --variant VCF/hapcaller.genotyped.vcf.gz -o VCF/hapcaller.indel.recal.select.vcf.gz
""" ;
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a prov:Entity;
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rdfs:comment """
gatk -Djava.io.tmpdir=VCF -XX:ParallelGCThreads=3 -Xmx3g -T SelectVariants -R ../testdata/human_g1k_v37.chr22.fasta --logging_level FATAL -selectType SNP --variant VCF/hapcaller.genotyped.vcf.gz -o VCF/hapcaller.snv.recal.select.vcf.gz
""" ;
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a prov:Activity ;
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gatk -Djava.io.tmpdir=VCF -XX:ParallelGCThreads=3 -Xmx3g -T VariantFiltration -R ../testdata/human_g1k_v37.chr22.fasta --logging_level FATAL --filterExpression 'QD < 2.0' --filterName 'FAILS_HARD_FILTER_SNP_QD' --filterExpression 'FS > 60.0' --filterName 'FAILS_HARD_FILTER_SNP_FS' --filterExpression 'MQ < 30.0' --filterName 'FAILS_HARD_FILTER_SNP_MQ' --filterExpression 'MQRankSum < -12.5' --filterName 'FAILS_HARD_FILTER_SNP_MQRankSum' --filterExpression 'ReadPosRankSum < -8.0' --filterName 'FAILS_HARD_FILTER_SNP_ReadPosRankSum' --variant VCF/hapcaller.snv.recal.select.vcf.gz -o VCF/hapcaller.snv.recal.filter.vcf.gz
""" ;
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gatk -Djava.io.tmpdir=VCF -XX:ParallelGCThreads=3 -Xmx3g -T VariantFiltration -R ../testdata/human_g1k_v37.chr22.fasta --logging_level FATAL --filterExpression 'QD < 2.0' --filterName 'FAILS_HARD_FILTER_INDEL_QD' --filterExpression 'FS > 200.0' --filterName 'FAILS_HARD_FILTER_INDEL_FS' --filterExpression 'ReadPosRankSum < -20.0' --filterName 'FAILS_HARD_FILTER_INDEL_ReadPosRankSum' --filterExpression 'SOR > 10.0' --filterName 'FAILS_HARD_FILTER_INDEL_SOR' --variant VCF/hapcaller.indel.recal.select.vcf.gz -o VCF/hapcaller.indel.recal.filter.vcf.gz
""" ;
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