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Exome sequencing workflow

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  prefix foaf <http://xmlns.com/foaf/0.1/>
  prefix bnode <http://openprovenance.org/provtoolbox/bnode/>
  prefix rdfs <http://www.w3.org/2000/01/rdf-schema#>
  prefix crypto <http://id.loc.gov/vocabulary/preservation/cryptographicHashFunctions#>
  prefix sym <http://fr.symetric/vocab#>
  prefix pre_4 <http://snakemake-provenance/Samples/Sample1/BAM/>
  prefix pre_7 <http://snakemake-provenance/Samples/Sample1/VCF/>
  prefix pre_6 <http://snakemake-provenance/Samples/Sample1/QC/>
  prefix pre_5 <http://snakemake-provenance/BED/>
  prefix rdf <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
  prefix pre_3 <http://snakemake-provenance/../testdata/>
  prefix pre_2 <http://snakemake-provenance#>
  prefix pre_1 <http://>
  prefix pre_0 <http://snakemake-provenance/>
  prefix sioc <http://rdfs.org/sioc/ns#>
  prefix dcterms <http://purl.org/dc/terms/>
  prefix pre_8 <http://snakemake-provenance/VCF/>
  
  wasGeneratedBy(pre_1:snakemake-provenance/Samples/Sample1/BAM/Sample1.merged.bam, pre_1:snakemake-provenance#activity-a8bc6f24-28be-4f69-8935-dac3bd21c7e5, -)
  wasGeneratedBy(pre_1:snakemake-provenance/VCF/hapcaller.indel.recal.filter.vcf.gz, pre_1:snakemake-provenance#activity-1b8b56a7-8090-46ce-b296-77185d2b41da, -)
  wasGeneratedBy(pre_1:snakemake-provenance/Samples/Sample1/BAM/Sample1.markdup.bam, pre_1:snakemake-provenance#activity-261c838b-5617-41b8-854d-b8d5d8d35720, -)
  wasGeneratedBy(pre_1:snakemake-provenance/VCF/hapcaller.snv.recal.select.vcf.gz.tbi, pre_1:snakemake-provenance#activity-e30231e3-60a8-49e5-97bb-fe3b3b9603ea, -)
  wasGeneratedBy(pre_1:snakemake-provenance/../testdata/human_g1k_v37.chr22.fasta, pre_1:snakemake-provenance#activity-13d827e1-f84f-4516-9389-60ccbbad8afa, -)
  wasGeneratedBy(pre_1:snakemake-provenance/Samples/Sample1/BAM/Sample1.final.bai, pre_1:snakemake-provenance#activity-81f3ecc0-d3ae-46f7-90b1-6fb5d07ae748, -)
  activity(pre_1:snakemake-provenance#activity-d44754c8-23b8-4ed6-a5d1-33ff46f90fc7, 2018-04-04T16:20:09.820406, 2018-04-04T16:20:09.820431, [pre_1:www.w3.org/2000/01/rdf-schema#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
	"""])
  activity(pre_1:snakemake-provenance#activity-09ba5fc3-2c1d-4961-9ef5-f2aa0851e513, 2018-04-04T16:19:15.889636, 2018-04-04T16:19:15.889661, [pre_1:www.w3.org/2000/01/rdf-schema#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
	"""])
  activity(pre_1:snakemake-provenance#activity-a8bc6f24-28be-4f69-8935-dac3bd21c7e5, 2018-04-04T16:18:42.096798, 2018-04-04T16:18:42.096819)
  activity(pre_1:snakemake-provenance#activity-261c838b-5617-41b8-854d-b8d5d8d35720, 2018-04-04T16:18:48.359872, 2018-04-04T16:18:48.359898, [pre_1:www.w3.org/2000/01/rdf-schema#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
	"""])
  activity(pre_1:snakemake-provenance#activity-1937d19a-45e3-4129-a7da-03b3ba8e6777, 2018-04-04T16:20:03.618600, 2018-04-04T16:20:03.618653, [pre_1:www.w3.org/2000/01/rdf-schema#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
	"""])
  activity(pre_1:snakemake-provenance#activity-5fef3da7-5391-4f26-a45a-587f49ac7c33, 2018-04-04T16:19:57.353788, 2018-04-04T16:19:57.353818)
  activity(pre_1:snakemake-provenance#activity-1b8b56a7-8090-46ce-b296-77185d2b41da, 2018-04-04T16:20:16.837222, 2018-04-04T16:20:16.837233, [pre_1:www.w3.org/2000/01/rdf-schema#comment="""
		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
	"""])
  activity(pre_1:snakemake-provenance#activity-8d26398a-112b-4d8e-968f-74ddd81b1f96, 2018-04-04T16:19:05.032708, 2018-04-04T16:19:05.032733, [pre_1:www.w3.org/2000/01/rdf-schema#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
	"""])
  activity(pre_1:snakemake-provenance#activity-945311db-8f46-440d-ad05-e8c93832006e, 2018-04-04T16:19:57.054054, 2018-04-04T16:19:57.054076, [pre_1:www.w3.org/2000/01/rdf-schema#comment="""
		gatk -Djava.io.tmpdir=Samples/Sample1/VCF -XX:ParallelGCThreads=5 -Xmx3g -T HaplotypeCaller 		-R ../testdata/human_g1k_v37.chr22.fasta 		--emitRefConfidence GVCF 		-variant_index_type LINEAR 		-variant_index_parameter 128000 		-stand_call_conf 30.0 		-nct 1 		-rf ReadLength 		-minRead 0 		-maxRead 10000 		-S SILENT 		-L:capture,BED BED/capture.extended1000.bed 		-I Samples/Sample1/BAM/Sample1.final.bam 		--dbsnp:dbsnp,VCF ../testdata/dbsnp_138.b37.chr22.recode.vcf.gz 		-o Samples/Sample1/VCF/Sample1.hapcaller.g.vcf
	"""])
  activity(pre_1:snakemake-provenance#activity-7922f888-30e3-4fd1-97ea-c1acde6ce2f2, 2018-04-04T16:18:38.899041, 2018-04-04T16:18:38.899068, [pre_1:www.w3.org/2000/01/rdf-schema#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
	"""])
  activity(pre_1:snakemake-provenance#activity-87303bf2-8fb2-47a7-a470-87c30cbee60c, 2018-04-04T16:20:13.333737, 2018-04-04T16:20:13.333758, [pre_1:www.w3.org/2000/01/rdf-schema#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
	"""])
  activity(pre_1:snakemake-provenance#activity-73212582-c497-4b3d-8691-302cfaa3c29b, 2018-04-04T16:18:57.941493, 2018-04-04T16:18:57.941516, [pre_1:www.w3.org/2000/01/rdf-schema#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
	"""])
  activity(pre_1:snakemake-provenance#activity-13d827e1-f84f-4516-9389-60ccbbad8afa, 2018-04-04T16:17:26.458524, 2018-04-04T16:17:26.458553, [pre_1:www.w3.org/2000/01/rdf-schema#comment="""
		gunzip -k ../testdata/human_g1k_v37.chr22.fasta.gz
	"""])
  activity(pre_1:snakemake-provenance#activity-651c204b-ce8b-4fcf-acdb-70b0dc4c4773, 2018-04-04T16:20:18.628519, 2018-04-04T16:20:18.628536, [pre_1:www.w3.org/2000/01/rdf-schema#comment="""
		gatk -Djava.io.tmpdir=VCF -XX:ParallelGCThreads=3 -Xmx3g -T CombineVariants 		-R ../testdata/human_g1k_v37.chr22.fasta 		--genotypemergeoption PRIORITIZE 	--rod_priority_list SNP,INDEL 		--variant:SNP VCF/hapcaller.snv.recal.filter.vcf.gz 		--variant:INDEL VCF/hapcaller.indel.recal.filter.vcf.gz 		-o VCF/hapcaller.recal.combined.vcf.gz
	"""])
  activity(pre_1:snakemake-provenance#activity-6ce42e0b-a885-4925-a357-01a9249a040c, 2018-04-04T16:20:21.092185, 2018-04-04T16:20:21.092220, [pre_1:www.w3.org/2000/01/rdf-schema#comment="""
		gatk -Djava.io.tmpdir=VCF -XX:ParallelGCThreads=3 -Xmx3g -T VariantAnnotator 		-R ../testdata/human_g1k_v37.chr22.fasta 		--variant VCF/hapcaller.recal.combined.vcf.gz 		-L VCF/hapcaller.recal.combined.vcf.gz 		--resource:gnomad ../testdata/gnomad.exomes.r2.0.1.sites.chr22.lite.vcf.gz 		--resourceAlleleConcordance 		-E gnomad.AF_AMR 		-E gnomad.AF_NFE 		-E gnomad.AF_Female 		-E gnomad.AF_ASJ 		-E gnomad.AF_OTH 		-E gnomad.AF_EAS 		-E gnomad.AF_SAS 		-E gnomad.AF_FIN 		-E gnomad.AF_Male 		--dbsnp ../testdata/dbsnp_138.b37.chr22.recode.vcf.gz 		-o VCF/hapcaller.recal.combined.annot.gnomad.vcf.gz
	"""])
  activity(pre_1:snakemake-provenance#activity-1e97329f-eb23-430b-a408-44e791d5af5d, 2018-04-04T16:18:27.214616, 2018-04-04T16:18:27.214639, [pre_1:www.w3.org/2000/01/rdf-schema#comment="""
		bwa index -a bwtsw ../testdata/human_g1k_v37.chr22.fasta
	"""])
  activity(pre_1:snakemake-provenance#activity-9a451c91-a37d-4168-93ba-56dd4ab22e19, 2018-04-04T16:18:48.467417, 2018-04-04T16:18:48.467434, [pre_1:www.w3.org/2000/01/rdf-schema#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
	"""])
  activity(pre_1:snakemake-provenance#activity-fdb368d2-ec97-4ee3-b58a-f18af1484afd, 2018-04-04T16:18:36.390303, 2018-04-04T16:18:36.390330, [pre_1:www.w3.org/2000/01/rdf-schema#comment="""
		bwa mem -t 1 -M 		-H '@CO	Project:test Sample:Sample1 Date:2018-04-04 CWD:/home/ubuntu/exome-pipeline/output Capture:{ name : captureName , description : exome capture test chr22 , path : ../testdata/Broad.human.exome.b37.chr22.bed}' 		-R '@RG	ID:Sample1	LB:Sample1	SM:Sample1	PL:Illumina	CN: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
	"""])
  activity(pre_1:snakemake-provenance#activity-3ace3a3c-30e7-4706-abd2-f7ffc1cdae7e, 2018-04-04T16:20:15.065591, 2018-04-04T16:20:15.065615, [pre_1:www.w3.org/2000/01/rdf-schema#comment="""
		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
	"""])
  activity(pre_1:snakemake-provenance#activity-3cbafc34-2134-488d-a9ed-316a579310ee, 2018-04-04T16:18:42.187623, 2018-04-04T16:18:42.187640, [pre_1:www.w3.org/2000/01/rdf-schema#comment="""
		tr -d '
' < ../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
	"""])
  activity(pre_1:snakemake-provenance#activity-28fbe7e0-0b9a-412b-8302-5d8e803ff2f2, 2018-04-04T16:20:21.097589, 2018-04-04T16:20:21.097610)
  activity(pre_1:snakemake-provenance#activity-81f3ecc0-d3ae-46f7-90b1-6fb5d07ae748, 2018-04-04T16:19:27.562206, 2018-04-04T16:19:27.562228, [pre_1:www.w3.org/2000/01/rdf-schema#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
	"""])
  activity(pre_1:snakemake-provenance#activity-ac9986a1-8797-4986-98e5-a936db1954c5, 2018-04-04T16:17:26.903339, 2018-04-04T16:17:26.903390, [pre_1:www.w3.org/2000/01/rdf-schema#comment="""
		samtools faidx ../testdata/human_g1k_v37.chr22.fasta
	"""])
  activity(pre_1:snakemake-provenance#activity-50db435e-6b29-4c30-8669-9834b01d7ce8, 2018-04-04T16:18:50.081432, 2018-04-04T16:18:50.081467)
  activity(pre_1:snakemake-provenance#activity-e30231e3-60a8-49e5-97bb-fe3b3b9603ea, 2018-04-04T16:20:11.641419, 2018-04-04T16:20:11.641446, [pre_1:www.w3.org/2000/01/rdf-schema#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
	"""])
  activity(pre_1:snakemake-provenance#activity-9bff5dd5-faf4-4e11-b3c0-2d0f75425297, 2018-04-04T16:18:42.923332, 2018-04-04T16:18:42.923360, [pre_1:www.w3.org/2000/01/rdf-schema#comment="""
		picard CreateSequenceDictionary REFERENCE=../testdata/human_g1k_v37.chr22.fasta OUTPUT=../testdata/human_g1k_v37.chr22.dict
	"""])
  entity(pre_1:snakemake-provenance/BED/capture.bed, [pre_1:id.loc.gov/vocabulary/preservation/cryptographicHashFunctions#sha512="28ebd6b14ac38c32935df05d2ad873651e9654b414a4c268dcdf585be6380c9d67ea0ad59365e3cc44dab46611ae4159bb9f0bd58d4f3028a9f4d85dfcb32768", pre_1:www.w3.org/ns/prov#label="BED/capture.bed"])
  entity(pre_1:snakemake-provenance/VCF/hapcaller.combined.g.vcf.gz, [pre_1:id.loc.gov/vocabulary/preservation/cryptographicHashFunctions#sha512="5e7285c72d9d268e28b4200c0d2560653b1cb2e907971bf8e486e2f4bd87981e6bf33f16a804b8511f801714f92b0d1a1942d1237f30add5e83295ca74b3243e", pre_1:www.w3.org/ns/prov#label="VCF/hapcaller.combined.g.vcf.gz"])
  entity(pre_1:snakemake-provenance/VCF/hapcaller.snv.recal.filter.vcf.gz, [pre_1:id.loc.gov/vocabulary/preservation/cryptographicHashFunctions#sha512="b700f7162449ffd06941a8275e1ddf4a332405a509c17288fe18052126bc1fe9377e2a65f759f33fd6013dfe4a897921968f9b3347abbd6b4928d4fbd3e9cfde", pre_1:www.w3.org/ns/prov#label="VCF/hapcaller.snv.recal.filter.vcf.gz"])
  entity(pre_1:snakemake-provenance/VCF/hapcaller.recal.combined.annot.gnomad.vcf.gz, [pre_1:id.loc.gov/vocabulary/preservation/cryptographicHashFunctions#sha512="59f396cb1368a3a6411acb9dda6e95aae8252ffbd40018cfa17054ea3963a54312bbdbc3577a7a5bbccfc2ce325a819bb05b5f05102abfd5f3dfd0957b5b65cb", pre_1:www.w3.org/ns/prov#label="VCF/hapcaller.recal.combined.annot.gnomad.vcf.gz"])
  entity(pre_1:snakemake-provenance/Samples/Sample1/QC/Sample1.markdup.metrics, [pre_1:id.loc.gov/vocabulary/preservation/cryptographicHashFunctions#sha512="d4dbdce4824ef7aab545a42b1992fe0faa0b10b10e19a36f824aaa59a8623c266240bb7136d305a0f62df3e1ad52f6252d65ea2f318f970e269b59cc482e388d", pre_1:www.w3.org/ns/prov#label="Samples/Sample1/QC/Sample1.markdup.metrics"])
  entity(pre_1:snakemake-provenance/Samples/Sample1/BAM/Sample1.realign.bam, [pre_1:id.loc.gov/vocabulary/preservation/cryptographicHashFunctions#sha512="dde4b344146fdf3e95b3b8f3d4f45a6718917f24caa8b14e996a4ac1d90335d24a1a5fe9c7c94d0beec5791c2ff7ba488ce53269e43b48cdcf416e32e1955ce3", pre_1:www.w3.org/ns/prov#label="Samples/Sample1/BAM/Sample1.realign.bam"])
  entity(pre_1:snakemake-provenance/VCF/hapcaller.recal.combined.vcf.gz, [pre_1:id.loc.gov/vocabulary/preservation/cryptographicHashFunctions#sha512="6582eaa196868bfd54389469664d99e3f83c89ea253b8c1b47263ce99ac514850eb0829d2553eb3cf2ad822d1a5c1c92fbb07a3dd91586be3a4d247e7e5562d3", pre_1:www.w3.org/ns/prov#label="VCF/hapcaller.recal.combined.vcf.gz"])
  entity(pre_1:snakemake-provenance/Samples/Sample1/BAM/Sample1.realign.bai, [pre_1:id.loc.gov/vocabulary/preservation/cryptographicHashFunctions#sha512="cba2502e3cd84d6a366f539ec364ded998d23a3417861178a5306da7f5c6d3b81536bb70829450a952a3fe74b8d7f499088dde40d83ba3a15a3c958274c2266e", pre_1:www.w3.org/ns/prov#label="Samples/Sample1/BAM/Sample1.realign.bai"])
  entity(pre_1:snakemake-provenance/Samples/Sample1/BAM/Sample1.p1.sorted.bam, [pre_1:id.loc.gov/vocabulary/preservation/cryptographicHashFunctions#sha512="a19b0c03ad288a032b6d1567adea8e66ee93b9dcce2cc1699b949d620fbe01439f0e70708d420fc61e3bb7051621a8879eb852c679b69ad97fd25831915b6ba6", pre_1:www.w3.org/ns/prov#label="Samples/Sample1/BAM/Sample1.p1.sorted.bam"])
  entity(pre_1:snakemake-provenance/VCF/hapcaller.snv.recal.select.vcf.gz.tbi, [pre_1:id.loc.gov/vocabulary/preservation/cryptographicHashFunctions#sha512="e264ecdf1abb04e8660cda330b07fe67b0cccb6d70dc814cc9260bd7336f2e40dda900dce61dba34d5217c32956ab93bb62ed58f2d1402eb6ed888fb1e3f2dd4", pre_1:www.w3.org/ns/prov#label="VCF/hapcaller.snv.recal.select.vcf.gz.tbi"])
  entity(pre_1:snakemake-provenance/Samples/Sample1/VCF/Sample1.hapcaller.g.vcf, [pre_1:id.loc.gov/vocabulary/preservation/cryptographicHashFunctions#sha512="28df1599bd0053ac08ce195db5750cf5c5f3a05597695449a2acee49b72245aee290bbc3f9ffcbe0f3f43b8c07156a175a424a25f2de53c326906340081d1c7b", pre_1:www.w3.org/ns/prov#label="Samples/Sample1/VCF/Sample1.hapcaller.g.vcf"])
  entity(pre_1:snakemake-provenance/../testdata/human_g1k_v37.chr22.fasta, [pre_1:id.loc.gov/vocabulary/preservation/cryptographicHashFunctions#sha512="ac169f3bee231f0a0d1cc93891aa49a9f81cc69afcd2914f0f02842513ebd5cf38e0dd62126e095dee9f145d9f498cd4e07fc155160552deaed6ebcb51dedcef", pre_1:www.w3.org/ns/prov#label="../testdata/human_g1k_v37.chr22.fasta"])
  entity(pre_1:snakemake-provenance/Samples/Sample1/BAM/Sample1.p1.aligned.sam, [pre_1:id.loc.gov/vocabulary/preservation/cryptographicHashFunctions#sha512="5e37bd28c55d6f016a43974263b2fdcb0996f2be269aa47f86c1c652df2afb471718a740454411f18ccd26608bdf40877f4c034e17e17cad1439c041002023dd", pre_1:www.w3.org/ns/prov#label="Samples/Sample1/BAM/Sample1.p1.aligned.sam"])
  entity(pre_1:snakemake-provenance/VCF/hapcaller.snv.recal.select.vcf.gz, [pre_1:id.loc.gov/vocabulary/preservation/cryptographicHashFunctions#sha512="540057520e8c7b5e86de75edd55be5ef4b21ef65c85b265a6c79b91f9905b7a9e5b6d583f8c3c421cb8504b85643c53a9a5796b44ec9fa8d7b41d3d883f1dba5", pre_1:www.w3.org/ns/prov#label="VCF/hapcaller.snv.recal.select.vcf.gz"])
  entity(pre_1:snakemake-provenance/BED/capture.extended1000.bed, [pre_1:id.loc.gov/vocabulary/preservation/cryptographicHashFunctions#sha512="e35f84eaf0fbfcfeb7a91d2d3c3b15e32ec3bc646e0d8cb03c1216f4141727ef3b58191cdb3829bf5098cefee07db21eb1a6e1b08955bb23ad6988000437e325", pre_1:www.w3.org/ns/prov#label="BED/capture.extended1000.bed"])
  entity(pre_1:snakemake-provenance/Samples/Sample1/BAM/Sample1.markdup.bai, [pre_1:id.loc.gov/vocabulary/preservation/cryptographicHashFunctions#sha512="93ffed428a9ab4679acea77511607ee5782338d812a431b52cea6a101e75e8a8a5b5d53e887c89da7a8e56ff1140b72dfbe1a42c8f94e07b435cad654344862d", pre_1:www.w3.org/ns/prov#label="Samples/Sample1/BAM/Sample1.markdup.bai"])
  entity(pre_1:snakemake-provenance/Samples/Sample1/BAM/Sample1.markdup.bam, [pre_1:id.loc.gov/vocabulary/preservation/cryptographicHashFunctions#sha512="26c0f2b2062bd82045d0b27e1f2b66fa9286cd99325e3468997df97cc1bfcb42340087564f5dab708718b54dc5c1181e7412fbc546d119f8df3734f6c2a6a3a8", pre_1:www.w3.org/ns/prov#label="Samples/Sample1/BAM/Sample1.markdup.bam"])
  entity(pre_1:snakemake-provenance/VCF/hapcaller.indel.recal.filter.vcf.gz.tbi, [pre_1:id.loc.gov/vocabulary/preservation/cryptographicHashFunctions#sha512="fe266f89aee3e47b5cf64e174a6a78295865b71ce1972443ec3e1d77f7777d7149e26c0edd9f81e1f529486b24fcd81a962f5cc082a416ad3116e1c181e88346", pre_1:www.w3.org/ns/prov#label="VCF/hapcaller.indel.recal.filter.vcf.gz.tbi"])
  entity(pre_1:snakemake-provenance, [pre_1:www.w3.org/ns/prov#type='pre_1:www.w3.org/ns/prov#Bundle'])
  entity(pre_1:snakemake-provenance/VCF/hapcaller.genotyped.vcf.gz, [pre_1:id.loc.gov/vocabulary/preservation/cryptographicHashFunctions#sha512="d5f69f9a5eaad45df87d2177558c34bb98653b7a56462575231064f2037bbeb8dcbcf6003e47e85bc1b17866909510cec93dd0cf1a1e9d87e701ba05bd7932fb", pre_1:www.w3.org/ns/prov#label="VCF/hapcaller.genotyped.vcf.gz"])
  entity(pre_1:snakemake-provenance/VCF/hapcaller.recal.combined.annot.gnomad.vcf.gz.tbi, [pre_1:id.loc.gov/vocabulary/preservation/cryptographicHashFunctions#sha512="ac4f074e7e2f34efd5f60ac71918a1303f762336cbe4f46bf363984d59142c912b572f59d171e22949940ca10c004ad42bf492aeac3f679f7e95d149c075b17a", pre_1:www.w3.org/ns/prov#label="VCF/hapcaller.recal.combined.annot.gnomad.vcf.gz.tbi"])
  entity(pre_1:snakemake-provenance/../testdata/human_g1k_v37.chr22.dict, [pre_1:id.loc.gov/vocabulary/preservation/cryptographicHashFunctions#sha512="d4d585066544087e2427f46be58cc68f64494a51998ba968270ec6792ba9c29fccf398977c964500976d1e9b392950cee4afa58fe4cc1184e9bff23ff4333a2e", pre_1:www.w3.org/ns/prov#label="../testdata/human_g1k_v37.chr22.dict"])
  entity(pre_1:snakemake-provenance/VCF/hapcaller.indel.recal.select.vcf.gz, [pre_1:id.loc.gov/vocabulary/preservation/cryptographicHashFunctions#sha512="bdea13d678ed71d386165dbbcc732cfaa4b6e3e7b8d76746f4801fc3d9a24c65c08fd179164568b3e169aa05ef1ae8ae4f63827e7e9e88f011e8337131324c34", pre_1:www.w3.org/ns/prov#label="VCF/hapcaller.indel.recal.select.vcf.gz"])
  entity(pre_1:snakemake-provenance/VCF/hapcaller.genotyped.vcf.gz.tbi, [pre_1:id.loc.gov/vocabulary/preservation/cryptographicHashFunctions#sha512="fd00675ec5a7563081b26fffb6e91e44c34f32b34df21f9f7990c70000b22c15e826ad17f5da099640144e663e282351cf5af5234cf4a00f78961787253f4f66", pre_1:www.w3.org/ns/prov#label="VCF/hapcaller.genotyped.vcf.gz.tbi"])
  entity(pre_1:snakemake-provenance/Samples/Sample1/BAM/Sample1.final.bai, [pre_1:id.loc.gov/vocabulary/preservation/cryptographicHashFunctions#sha512="a264e59320feef5195aae7a13236c3df8ae1ac285b391cc5c1e30186305d62b1e8f1e961693a5cc7397de5e9ed53339448dca0b9dd9b8afa640b65b5821a7762", pre_1:www.w3.org/ns/prov#label="Samples/Sample1/BAM/Sample1.final.bai"])
  entity(pre_1:snakemake-provenance/VCF/hapcaller.indel.recal.select.vcf.gz.tbi, [pre_1:id.loc.gov/vocabulary/preservation/cryptographicHashFunctions#sha512="1abac388f58f1cc738a50f3b102346301aa8b98c54ed5cf2990bcabc2ab4b654ac2c6af31ac81b37ae91e5ca7fa726faa661cba7dd002115d1216302efcff234", pre_1:www.w3.org/ns/prov#label="VCF/hapcaller.indel.recal.select.vcf.gz.tbi"])
  entity(pre_1:snakemake-provenance/Samples/Sample1/BAM/Sample1.recal.table, [pre_1:id.loc.gov/vocabulary/preservation/cryptographicHashFunctions#sha512="996b8b87a96b58a64d88c95409bcd5b93ae2452926ee8fa91d875b08fa4b42b41727e72e71fb9bcb80ed18295d82b36d24f4528bd65931c4bccfc4565e5c1ef1", pre_1:www.w3.org/ns/prov#label="Samples/Sample1/BAM/Sample1.recal.table"])
  entity(pre_1:snakemake-provenance/Samples/Sample1/VCF/Sample1.hapcaller.g.vcf.idx, [pre_1:id.loc.gov/vocabulary/preservation/cryptographicHashFunctions#sha512="c714552e940f7a058f666b25844c5ff52c53b80485db7ad9d3ab99041c11f43f99f38bad93e49b9dd9905050fe8e6c58a43ebc6e8aed0f8d68c3efbb87f11336", pre_1:www.w3.org/ns/prov#label="Samples/Sample1/VCF/Sample1.hapcaller.g.vcf.idx"])
  entity(pre_1:snakemake-provenance/VCF/gvcf.list, [pre_1:id.loc.gov/vocabulary/preservation/cryptographicHashFunctions#sha512="eff789b5f1e9ca98b152b3fbe8ab44289e5e220e179b3d4797311254f95b2b5108748277fb3613f9917050958482660f1ceea2f1a0b52da74665a9f945cf6ad7", pre_1:www.w3.org/ns/prov#label="VCF/gvcf.list"])
  entity(pre_1:snakemake-provenance/Samples/Sample1/BAM/Sample1.merged.bai, [pre_1:id.loc.gov/vocabulary/preservation/cryptographicHashFunctions#sha512="7ea76d647dc6a2155ca96eb8e4dbde8bf6b29e257e4ef6472fc30d603ac2156026ce589394a40f966d6e0ee9bdbb3450c18940226321e10ba56e33c689df3504", pre_1:www.w3.org/ns/prov#label="Samples/Sample1/BAM/Sample1.merged.bai"])
  entity(pre_1:snakemake-provenance/VCF/hapcaller.recal.combined.vcf.gz.tbi, [pre_1:id.loc.gov/vocabulary/preservation/cryptographicHashFunctions#sha512="a3fdd55de56575326af2552761dcc557fc40b90977905f9a795813cac22c108a033720905e78af1ff619c28f754267ae1721b04b54916d936e2b0c55b0f4331a", pre_1:www.w3.org/ns/prov#label="VCF/hapcaller.recal.combined.vcf.gz.tbi"])
  entity(pre_1:snakemake-provenance/gatkPresent.txt, [pre_1:id.loc.gov/vocabulary/preservation/cryptographicHashFunctions#sha512="cf83e1357eefb8bdf1542850d66d8007d620e4050b5715dc83f4a921d36ce9ce47d0d13c5d85f2b0ff8318d2877eec2f63b931bd47417a81a538327af927da3e", pre_1:www.w3.org/ns/prov#label="gatkPresent.txt"])
  entity(pre_1:snakemake-provenance/VCF/hapcaller.snv.recal.filter.vcf.gz.tbi, [pre_1:id.loc.gov/vocabulary/preservation/cryptographicHashFunctions#sha512="cfaae7834d45b61e631d051c63dbcd1f94f41dc2739806c6e4fae6fca9f16e53545cc15cbf2acd67b0edc7056b118ce41412b31640bde905c7055a75629c5165", pre_1:www.w3.org/ns/prov#label="VCF/hapcaller.snv.recal.filter.vcf.gz.tbi"])
  entity(pre_1:snakemake-provenance/Samples/Sample1/BAM/Sample1.merged.bam, [pre_1:id.loc.gov/vocabulary/preservation/cryptographicHashFunctions#sha512="50d6f5b257719ba3e77fde9fd20346928798bfda16f35834ebfade42d1117cee0528644d5c04874798725e2711573d028de8f7f86d2ff563244845f49e029451", pre_1:www.w3.org/ns/prov#label="Samples/Sample1/BAM/Sample1.merged.bam"])
  entity(pre_1:snakemake-provenance/Samples/Sample1/BAM/Sample1.realign.intervals, [pre_1:id.loc.gov/vocabulary/preservation/cryptographicHashFunctions#sha512="364dc7011bdf3aa66b6703477eb444c10b7df366c0fc4a1e132a3a4f06ea0c7bc0d1d9ded8b6fb637f8e98b0c038a0faf105477afee6ed88a948232577a1d19a", pre_1:www.w3.org/ns/prov#label="Samples/Sample1/BAM/Sample1.realign.intervals"])
  entity(pre_1:snakemake-provenance/../testdata/human_g1k_v37.chr22.fasta.bwt, [pre_1:id.loc.gov/vocabulary/preservation/cryptographicHashFunctions#sha512="88153374f3dd716703be07cc72c2252ca34c16432ac39b8f771600c7435fba1e0f17a19c0310320c19beb65bcc219c91349d3a11a489dc6b963bf042befe60cc", pre_1:www.w3.org/ns/prov#label="../testdata/human_g1k_v37.chr22.fasta.bwt"])
  entity(pre_1:snakemake-provenance/VCF/hapcaller.indel.recal.filter.vcf.gz, [pre_1:id.loc.gov/vocabulary/preservation/cryptographicHashFunctions#sha512="d72e63fbf687e9b9276800c233d4fc2cfe36489429eca5b9ce5e99ca14840ae1095e119df7867e474b42e71b2c7c157420babc6385f2426b4b8d6d7c07cdba8c", pre_1:www.w3.org/ns/prov#label="VCF/hapcaller.indel.recal.filter.vcf.gz"])
  entity(pre_1:snakemake-provenance/Samples/Sample1/BAM/Sample1.final.bam, [pre_1:id.loc.gov/vocabulary/preservation/cryptographicHashFunctions#sha512="757b6ca7b562f2e15d9796e1f43b429a255eb9dff1b7ce14a556693d031673d9fb27fec05dbae95d2b42c733517537b6da7779ad9b8b421d624ddefc46ba99bd", pre_1:www.w3.org/ns/prov#label="Samples/Sample1/BAM/Sample1.final.bam"])
  entity(pre_1:snakemake-provenance/VCF/hapcaller.combined.g.vcf.gz.tbi, [pre_1:id.loc.gov/vocabulary/preservation/cryptographicHashFunctions#sha512="a28af084d53d4d105fd3ef479e7ae41c95db2d724010b1197bc49b9986a3bcf0f6c641c9ee291e053d8b7a26f3c4eb2de116e1f639a66d3e21b1c29f587de8ce", pre_1:www.w3.org/ns/prov#label="VCF/hapcaller.combined.g.vcf.gz.tbi"])
  entity(pre_1:snakemake-provenance/../testdata/human_g1k_v37.chr22.fasta.fai, [pre_1:id.loc.gov/vocabulary/preservation/cryptographicHashFunctions#sha512="842a03973ac584fb89d9e6add7570d32aba1405db83452f7c7333a826d458a6b0f74925d8363e98b1b157de32d5212ecaf625044b65ffb9f330b86649352d00d", pre_1:www.w3.org/ns/prov#label="../testdata/human_g1k_v37.chr22.fasta.fai"])
  agent(pre_1:snakemake-provenance/:ubuntu, [pre_1:www.w3.org/ns/prov#type='pre_1:www.w3.org/ns/prov#Person'])
  wasAttributedTo(pre_1:snakemake-provenance/VCF/hapcaller.combined.g.vcf.gz, pre_1:snakemake-provenance#combineGVCF)
  wasAttributedTo(pre_1:snakemake-provenance/../testdata/human_g1k_v37.chr22.fasta.bwt, pre_1:snakemake-provenance#bwaIndex)
  wasAttributedTo(pre_1:snakemake-provenance/Samples/Sample1/BAM/Sample1.realign.bam, pre_1:snakemake-provenance#indelRealign)
  wasAttributedTo(pre_1:snakemake-provenance/Samples/Sample1/VCF/Sample1.hapcaller.g.vcf.idx, pre_1:snakemake-provenance#haplotypeCaller)
  wasAttributedTo(pre_1:snakemake-provenance/Samples/Sample1/BAM/Sample1.p1.sorted.bam, pre_1:snakemake-provenance#sort)
  wasAttributedTo(pre_1:snakemake-provenance/Samples/Sample1/BAM/Sample1.merged.bai, pre_1:snakemake-provenance#merge)
  wasAttributedTo(pre_1:snakemake-provenance/Samples/Sample1/BAM/Sample1.realign.intervals, pre_1:snakemake-provenance#realignTargetCreator)
  wasAttributedTo(pre_1:snakemake-provenance/VCF/hapcaller.indel.recal.select.vcf.gz, pre_1:snakemake-provenance#selectIndels)
  wasAttributedTo(pre_1:snakemake-provenance/Samples/Sample1/VCF/Sample1.hapcaller.g.vcf, pre_1:snakemake-provenance#haplotypeCaller)
  wasAttributedTo(pre_1:snakemake-provenance/VCF/hapcaller.genotyped.vcf.gz.tbi, pre_1:snakemake-provenance#genotypeGVCF)
  wasAttributedTo(pre_1:snakemake-provenance/VCF/hapcaller.recal.combined.vcf.gz.tbi, pre_1:snakemake-provenance#combineVCF)
  wasAttributedTo(pre_1:snakemake-provenance/VCF/hapcaller.snv.recal.select.vcf.gz, pre_1:snakemake-provenance#selectSNVs)
  wasAttributedTo(pre_1:snakemake-provenance/Samples/Sample1/BAM/Sample1.merged.bam, pre_1:snakemake-provenance#merge)
  wasAttributedTo(pre_1:snakemake-provenance/VCF/hapcaller.indel.recal.filter.vcf.gz, pre_1:snakemake-provenance#filterIndels)
  wasAttributedTo(pre_1:snakemake-provenance/VCF/hapcaller.indel.recal.filter.vcf.gz.tbi, pre_1:snakemake-provenance#filterIndels)
  wasAttributedTo(pre_1:snakemake-provenance/../testdata/human_g1k_v37.chr22.fasta.fai, pre_1:snakemake-provenance#genomeIndex)
  wasAttributedTo(pre_1:snakemake-provenance/Samples/Sample1/BAM/Sample1.realign.bai, pre_1:snakemake-provenance#indelRealign)
  wasAttributedTo(pre_1:snakemake-provenance/Samples/Sample1/BAM/Sample1.final.bam, pre_1:snakemake-provenance#baseRecalibration)
  wasAttributedTo(pre_1:snakemake-provenance/../testdata/human_g1k_v37.chr22.fasta, pre_1:snakemake-provenance#unzipGenome)
  wasAttributedTo(pre_1:snakemake-provenance/VCF/hapcaller.snv.recal.filter.vcf.gz, pre_1:snakemake-provenance#filterSNVs)
  wasAttributedTo(pre_1:snakemake-provenance/BED/capture.extended1000.bed, pre_1:snakemake-provenance#extendBed)
  wasAttributedTo(pre_1:snakemake-provenance/VCF/hapcaller.recal.combined.annot.gnomad.vcf.gz, pre_1:snakemake-provenance#freqGNOMAD)
  wasAttributedTo(pre_1:snakemake-provenance/Samples/Sample1/QC/Sample1.markdup.metrics, pre_1:snakemake-provenance#markDuplicates)
  wasAttributedTo(pre_1:snakemake-provenance/Samples/Sample1/BAM/Sample1.recal.table, pre_1:snakemake-provenance#createBaseRecalibrationTable)
  wasAttributedTo(pre_1:snakemake-provenance, pre_1:snakemake-provenance/:ubuntu)
  wasAttributedTo(pre_1:snakemake-provenance/VCF/hapcaller.snv.recal.filter.vcf.gz.tbi, pre_1:snakemake-provenance#filterSNVs)
  wasAttributedTo(pre_1:snakemake-provenance/VCF/hapcaller.combined.g.vcf.gz.tbi, pre_1:snakemake-provenance#combineGVCF)
endDocument
        
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wasGeneratedBy6
agent1
entity40
wasAttributedTo27
activity26