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added filtering to somatic mutation calls; fixed jsons to repair miss…
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…ing resources in fusion and rnaseqvar pipelines
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Justin Britt Lack committed Dec 22, 2017
1 parent 7df59ea commit f6614e8
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Showing 8 changed files with 60 additions and 54 deletions.
2 changes: 1 addition & 1 deletion Results-template/Scripts/prep_mafs.pl
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Expand Up @@ -102,7 +102,7 @@
my $col='';

my $z=0;
for ($z=0; $z<@columns; $z++)
for ($z=0; $z<@columns; $z++) {
if ($columns[$z] eq 'ExAC_AF') {
$col=$z;
last;
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6 changes: 3 additions & 3 deletions Rules/all-exomeseq-somatic-tumoronly.rl
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Expand Up @@ -14,7 +14,7 @@ if config['project']['annotation'] == "hg19":
config['project']['workpath']+"/cnvkit_out/CNVkit_summary_heatmap.pdf",
config['project']['workpath']+"/sample_network.bmp",
config['project']['workpath']+"/mutect2_out/mutect2_variants.database",
config['project']['workpath']+"/mutect2_out/oncotator_out/mutect2_variants.maf",
config['project']['workpath']+"/mutect2_out/oncotator_out/mutect2_filtered.maf",
config['project']['workpath']+"/mutect2_out/mutsigCV_out/somatic.sig_genes.txt",
config['project']['workpath']+"/exome_targets.bed",
expand("manta_out/{s}/results/variants/candidateSV.vcf.gz", s=samples),
Expand Down Expand Up @@ -42,7 +42,7 @@ elif config['project']['annotation'] == "hg38":
config['project']['workpath']+"/cnvkit_out/CNVkit_summary_heatmap.pdf",
config['project']['workpath']+"/sample_network.bmp",
config['project']['workpath']+"/mutect2_out/mutect2_variants.database",
config['project']['workpath']+"/mutect2_out/oncotator_out/mutect2_variants.maf",
config['project']['workpath']+"/mutect2_out/oncotator_out/mutect2_filtered.maf",
config['project']['workpath']+"/mutect2_out/mutsigCV_out/somatic.sig_genes.txt",
config['project']['workpath']+"/exome_targets.bed",
expand("manta_out/{s}/results/variants/candidateSV.vcf.gz", s=samples),
Expand All @@ -69,7 +69,7 @@ elif config['project']['annotation'] == "mm10":
config['project']['workpath']+"/mutect2_out/mutect2_oncoplot.pdf",
config['project']['workpath']+"/mutect2_out/mutect2_variants.database",
config['project']['workpath']+"/sample_network.bmp",
# config['project']['workpath']+"/mutect2_out/oncotator_out/mutect2_variants.maf",
# config['project']['workpath']+"/mutect2_out/oncotator_out/mutect2_filtered.maf",
config['project']['workpath']+"/mutect2_out/mutsigCV_out/somatic.sig_genes.txt",
config['project']['workpath']+"/exome_targets.bed",
expand("manta_out/{s}/results/variants/candidateSV.vcf.gz", s=samples),
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2 changes: 1 addition & 1 deletion Rules/gatk.rnaseqvar.haplotype.caller.rl
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Expand Up @@ -2,7 +2,7 @@ rule gatk_rnaseqvar_haplotype_caller:
input: lambda wildcards: config['project']['units'][wildcards.x]+".recal.bam"
output:"{x}.g.vcf"
params: gres="lscratch:100",gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],snpsites=config['references'][pfamily]['SNPSITES'],rname="pl:rnahapcall"
threads: 4
threads: 2
shell: "module load GATK/3.6; GATK -m 24g HaplotypeCaller -R {params.genome} -I {input} --read_filter BadCigar -dontUseSoftClippedBases -stand_call_conf 20.0 -stand_emit_conf 20.0 --emitRefConfidence GVCF --annotation Coverage -A FisherStrand -A HaplotypeScore -A MappingQualityRankSumTest -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest --variant_index_type LINEAR --dbsnp {params.snpsites} --variant_index_parameter 128000 -nct {threads} -o {output[0]}"


2 changes: 1 addition & 1 deletion Rules/maftools_tumoronly.rl
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@@ -1,5 +1,5 @@
rule maftools_tumoronly:
input: mutect2mafs=expand(config['project']['workpath']+"/mutect2_out/oncotator_out/{x}.maf"),
input: mafs=expand(config['project']['workpath']+"/mutect2_out/oncotator_out/{s}.maf",s=samples),
output: mutect2maf=config['project']['workpath']+"/mutect2_out/oncotator_out/mutect2_filtered.maf",
mutect2summary=config['project']['workpath']+"/mutect2_out/mutect2_maf_summary.pdf",
mutect2oncoprint=config['project']['workpath']+"/mutect2_out/mutect2_oncoplot.pdf",
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2 changes: 1 addition & 1 deletion Rules/qualimap.rl
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Expand Up @@ -4,4 +4,4 @@ rule qualimap:
output: dir="QC/{x}.qualimapReport",txt="QC/{x}.qualimapReport/genome_results.txt"
threads: 8
params: qualimap=config['bin'][pfamily]['QUALIMAP'],organism=config['references'][pfamily]['ORGANISM'],regions="exome_targets.bed",rname="pl:qualimap"
shell: "{params.qualimap} bamqc -bam {input.bam} -c gd {params.organism} -ip -outdir {output.dir} -gff {params.regions} -outfile report.pdf -outformat PDF -nt {threads} --skip-duplicated -nw 500 -p NON-STRAND-SPECIFIC"
shell: "{params.qualimap} bamqc -bam {input.bam} -c gd {params.organism} -ip -outdir {output.dir} -gff {params.regions} -outformat HTML -nt {threads} --skip-duplicated -nw 500 -p NON-STRAND-SPECIFIC"
33 changes: 18 additions & 15 deletions hg19.json
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Expand Up @@ -153,50 +153,53 @@
"KARYOBEDS": "/data/CCBR_Pipeliner/db/PipeDB/dev/karyobeds/hg.v19/",
"RSEMREF": "/data/CCBR_Pipeliner/db/PipeDB/Rnaseq/rsem1.3.0/human_gencode",
"RRNALIST": "/data/CCBR_Pipeliner/db/PipeDB/dev/Hg19.rRNA.interval_list_v3",
"ADMIXTUREKEY": "/data/CCBR_Pipeliner/db/PipeDB/lib/1k_genomes_superpop_key.txt",
"ADMIXTUREREFS": "5",
"ORGANISM": "HUMAN",
# "FASTQ_SCREEN_CONFIG": "/data/CCBR_Pipeliner/db/PipeDB/lib/fastq_screen.conf",
# "FASTAWITHADAPTERSETC": "/data/CCBR_Pipeliner/dev/RNA-Seq-pipeline/ver2/TruSeq_and_nextera_adapters_new.fa",
"FASTAWITHADAPTERSETC": "/data/CCBR_Pipeliner/db/PipeDB/dev/TruSeq_and_nextera_adapters_new.fa",
# "GTFFILE2": "/data/CCBR_Pipeliner/db/PipeDB/lib/hs37d5/annotation/gencode.v19.annotation.gtf",
"FUSIONGTFFILE": "/data/CCBR_Pipeliner/db/PipeDB/lib/GENCODE_GRCh37_ref_annot.gtf",
# "REFFLAT2": "/data/CCBR_Pipeliner/db/PipeDB/lib/hs37d5/annotation/refFlatHg19.txt",
# "SALMONREF": "/data/CCBR_Pipeliner/db/PipeDB/Rnaseq/rsem1.3.0/human_gencode.transcripts.fa",
# "STARREF": "/data/CCBR_Pipeliner/db/PipeDB/lib/Star_refs/hs37d5/genes-",
"STARREF": "/data/CCBR_Pipeliner/db/PipeDB/lib/Star_refs/hs37d5/genes-",
# "RRNALIST2": "/data/CCBR_Pipeliner/db/PipeDB/lib/hs37d5/annotation/gencode.v19.annotation.gtf.rRNA.interval_list",
"STARFUSIONLIB": "/data/CCBR_Pipeliner/db/PipeDB/lib/GRCh37_gencode_v19_CTAT_lib_July272016_prebuilt",
"FUSCATCHDAT": "/usr/local/apps/fusioncatcher/0.99.7b/fusioncatcher/data/ensembl_v86",
"FUSCATCHCONFIG": "/data/CCBR_Pipeliner/db/PipeDB/lib/hg19_hg38_configuration.cfg",
"FASTQ_SCREEN_CONFIG": "/data/CCBR_Pipeliner/db/PipeDB/lib/fastq_screen.conf",
# "GENOME": "/data/CCBR_Pipeliner/db/PipeDB/lib/hs37d5.fa",
"GENOME": "/data/CCBR_Pipeliner/db/PipeDB/lib/hs37d5.fa",
# "INDELSITES": "/fdb/GATK_resource_bundle/b37/Mills_and_1000G_gold_standard.indels.b37.vcf",
# "KNOWNANCESTRY": "/data/CCBR_Pipeliner/db/PipeDB/lib/1k_genomes_phase3_autosomes.vcf.gz",
# "KNOWNVCF": "/data/CCBR_Pipeliner/db/PipeDB/lib/1k_genomes_compSet.vcf",
# "KNOWNVCF2": "/fdb/GATK_resource_bundle/b37-2.8/1000G_phase3_v4_20130502.sites.vcf.gz",
# "SNPSITES": "/fdb/GATK_resource_bundle/b37/dbsnp_138.b37.vcf",
# "KNOWNINDELS": "-known /fdb/GATK_resource_bundle/b37/Mills_and_1000G_gold_standard.indels.b37.vcf -known /fdb/GATK_resource_bundle/b37/1000G_phase1.indels.b37.vcf",
# "KNOWNRECAL": "-knownSites /fdb/GATK_resource_bundle/b37/dbsnp_138.b37.vcf -knownSites /fdb/GATK_resource_bundle/b37/Mills_and_1000G_gold_standard.indels.b37.vcf -knownSites /fdb/GATK_resource_bundle/b37/1000G_phase1.indels.b37.vcf",
"KNOWNANCESTRY": "/data/CCBR_Pipeliner/db/PipeDB/lib/1k_genomes_phase3_autosomes.vcf.gz",
"KNOWNVCF": "/data/CCBR_Pipeliner/db/PipeDB/lib/1k_genomes_compSet.vcf",
"KNOWNVCF2": "/fdb/GATK_resource_bundle/b37-2.8/1000G_phase3_v4_20130502.sites.vcf.gz",
"SNPSITES": "/fdb/GATK_resource_bundle/b37/dbsnp_138.b37.vcf",
"KNOWNINDELS": "-known /fdb/GATK_resource_bundle/b37/Mills_and_1000G_gold_standard.indels.b37.vcf -known /fdb/GATK_resource_bundle/b37/1000G_phase1.indels.b37.vcf",
# "THETASNPS": "/data/CCBR_Pipeliner/db/PipeDB/lib/hg19_theta_SNPfile.txt",
# "INDELSITES2": "/fdb/GATK_resource_bundle/b37/1000G_phase1.indels.b37.vcf",
# "ALVIEWGENOME": "hg19",
"INDELSITES2": "/fdb/GATK_resource_bundle/b37/1000G_phase1.indels.b37.vcf",
"ALVIEWGENOME": "hg19",
"ONCOFUSEBUILD": "hg19",
# "EXONS": "/data/CCBR_Pipeliner/db/PipeDB/lib/hg19.exons.bed",
"KNOWNRECAL": "-knownSites /fdb/GATK_resource_bundle/b37/dbsnp_138.b37.vcf -knownSites /fdb/GATK_resource_bundle/b37/Mills_and_1000G_gold_standard.indels.b37.vcf -knownSites /fdb/GATK_resource_bundle/b37/1000G_phase1.indels.b37.vcf",
"EXONS": "/data/CCBR_Pipeliner/db/PipeDB/lib/hg19.exons.bed",
# "ANNDIR": "/data/CCBR_Pipeliner/db/PipeDB/AnnovarDB/",
# "tg_GS_INDELS": "/fdb/GATK_resource_bundle/hg19-2.8/Mills_and_1000G_gold_standard.indels.hg19.vcf.gz",
# "tg_PHASE_INDELS": "/fdb/GATK_resource_bundle/hg19-2.8/1000G_phase1.indels.hg19.vcf.gz",
# "SNP138": "/fdb/GATK_resource_bundle/hg19-2.8/dbsnp_138.hg19.vcf.gz",
# "HAPMAP": "/fdb/GATK_resource_bundle/hg19-2.8/hapmap_3.3.hg19.vcf.gz",
# "B1K": "/fdb/GATK_resource_bundle/hg19-2.8/1000G_phase1.snps.high_confidence.hg19.vcf.gz",
# "OMNI": "/fdb/GATK_resource_bundle/hg19-2.8/1000G_omni2.5.hg19.vcf.gz",
# "adapter.file": "/data/CCBR_Pipeliner/db/PipeDB/dev/TruSeq_and_nextera_adapters.ngsqc.dat",
"adapter.file": "/data/CCBR_Pipeliner/db/PipeDB/dev/TruSeq_and_nextera_adapters.ngsqc.dat",
"fastqc.adapters": "/data/CCBR_Pipeliner/db/PipeDB/dev/fastqc.adapters",
"trimmomatic.adapters": "/data/CCBR_Pipeliner/db/PipeDB/dev/adapters2.fa",
# "ORGANISM": "HUMAN",
# "AVIASET": "hg19",
"AVIASET": "hg19",
# "ADAPTER1": "AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC",
# "ADAPTER2": "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT",
# "nextera1": "CTGTCTCTTATACACATCTCCGAGCCCACGAGAC",
# "nextera2": "CTGTCTCTTATACACATCTGACGCTGCCGACGA",
# "DB29": "/data/CCBR_Pipeliner/db/PipeDB/snpEff_db/dbNSFP2.9.txt.gz",
# "SNPEFF_CONFIG": "/usr/local/apps/snpEff/4.2/snpEff.config",
"SNPEFF_CONFIG": "/usr/local/apps/snpEff/4.2/snpEff.config",
"SNPEFF_GENOME": "GRCh37.75",
# "SELECTDB": "SIFT_score,SIFT_pred,Polyphen2_HVAR_score,Polyphen2_HVAR_pred,LRT_score,LRT_pred,GERP++_RS,MutationAssessor_score,MutationAssessor_pred,1000Gp1_AF,1000Gp1_EUR_AF,ESP6500_EA_AF,ESP6500_AA_AF",
# "REGULOMEDB": "/data/CCBR_Pipeliner/db/PipeDB/lib/snpEff_db/RegulomeDB.bed",
#>>>>>>> FETCH_HEAD
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33 changes: 18 additions & 15 deletions hg38.json
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Expand Up @@ -145,49 +145,52 @@
"RSEMREF": "/data/CCBR_Pipeliner/db/PipeDB/Rnaseq/rsem1.3.0/hg38_R26/human_gencode",
"STARDIR": "/fdb/STAR_indices/2.5.2b/GENCODE/Gencode_human/release_26/genes-",
"RRNALIST": "/data/CCBR_Pipeliner/db/PipeDB/dev/Hg38.rRNA.interval_list_R26",
"ADMIXTUREKEY": "/data/CCBR_Pipeliner/db/PipeDB/lib/1k_genomes_superpop_key.txt",
"ADMIXTUREREFS": "5",
"FASTQ_SCREEN_CONFIG": "/data/CCBR_Pipeliner/db/PipeDB/lib/fastq_screen.conf",
"FUSIONGTFFILE": "/fdb/GENCODE/Gencode_human/release_26/gencode.v26.annotation.gtf",
# "REFFLAT2": "/data/CCBR_Pipeliner/db/PipeDB/dev/refFlatHg38_R26.txt",
# "SALMONREF": "/data/CCBR_Pipeliner/db/PipeDB/Rnaseq/rsem1.3.0/hg38_R26/human_gencode.transcripts.fa",
# "FASTAWITHADAPTERSETC": "/data/CCBR_Pipeliner/dev/RNA-Seq-pipeline/ver2/TruSeq_and_nextera_adapters_new.fa",
"FASTAWITHADAPTERSETC": "/data/CCBR_Pipeliner/db/PipeDB/dev/TruSeq_and_nextera_adapters_new.fa",
# "STARREF": "/fdb/STAR_indices/2.5.2b/GENCODE/Gencode_human/release_26/genes-",
"STARREF": "/fdb/STAR_indices/2.5.2b/GENCODE/Gencode_human/release_26/genes-",
# "RRNALIST2": "/data/CCBR_Pipeliner/db/PipeDB/dev/Hg38.rRNA.interval_list_R26",
"STARFUSIONLIB": "/data/CCBR_Pipeliner/db/PipeDB/lib/GRCh38_gencode_v24_CTAT_lib_Mar292017_prebuilt",
"FUSCATCHDAT": "/usr/local/apps/fusioncatcher/0.99.7b/fusioncatcher/data/ensembl_v86",
"FUSCATCHCONFIG": "/data/CCBR_Pipeliner/db/PipeDB/lib/hg19_hg38_configuration.cfg",
# "GENOME": "/fdb/GENCODE/Gencode_human/release_26/GRCh38.primary_assembly.genome.fa",
"GENOME": "/fdb/GENCODE/Gencode_human/release_26/GRCh38.primary_assembly.genome.fa",
# "INDELSITES": "/fdb/GATK_resource_bundle/hg38bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz",
# "KNOWNANCESTRY": "/data/CCBR_Pipeliner/db/PipeDB/lib/1k_genomes_phase3_autosomes.hg38.vcf.gz",
# "KNOWNVCF": "/data/CCBR_Pipeliner/db/PipeDB/lib/1k_genomes_compSet.vcf",
# "KNOWNVCF2": "/fdb/GATK_resource_bundle/hg38bundle/1000G_phase1.snps.high_confidence.hg38.vcf.gz",
# "SNPSITES": "/fdb/GATK_resource_bundle/hg38bundle/dbsnp_146.hg38.vcf.gz",
# "KNOWNINDELS": "-known /fdb/GATK_resource_bundle/hg38bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz -known /data/CCBR_Pipeliner/db/PipeDB/lib/ALL.wgs.1000G_phase3.GRCh38.ncbi_remapper.20150424.shapeit2_indels.vcf.gz",
# "KNOWNRECAL": "-knownSites /fdb/GATK_resource_bundle/hg38bundle/dbsnp_138.hg38.vcf.gz -knownSites /fdb/GATK_resource_bundle/hg38bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz -knownSites /data/CCBR_Pipeliner/db/PipeDB/lib/ALL.wgs.1000G_phase3.GRCh38.ncbi_remapper.20150424.shapeit2_indels.vcf.gz",
"KNOWNANCESTRY": "/data/CCBR_Pipeliner/db/PipeDB/lib/1k_genomes_phase3_autosomes.hg38.vcf.gz",
"KNOWNVCF": "/data/CCBR_Pipeliner/db/PipeDB/lib/1k_genomes_compSet.vcf",
"KNOWNVCF2": "/fdb/GATK_resource_bundle/hg38bundle/1000G_phase1.snps.high_confidence.hg38.vcf.gz",
"SNPSITES": "/fdb/GATK_resource_bundle/hg38bundle/dbsnp_146.hg38.vcf.gz",
"KNOWNINDELS": "-known /fdb/GATK_resource_bundle/hg38bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz -known /data/CCBR_Pipeliner/db/PipeDB/lib/ALL.wgs.1000G_phase3.GRCh38.ncbi_remapper.20150424.shapeit2_indels.vcf.gz",
"KNOWNRECAL": "-knownSites /fdb/GATK_resource_bundle/hg38bundle/dbsnp_138.hg38.vcf.gz -knownSites /fdb/GATK_resource_bundle/hg38bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz -knownSites /data/CCBR_Pipeliner/db/PipeDB/lib/ALL.wgs.1000G_phase3.GRCh38.ncbi_remapper.20150424.shapeit2_indels.vcf.gz",
# "THETASNPS": "/data/CCBR_Pipeliner/db/PipeDB/lib/hg38_theta_SNPfile.txt",
# "INDELSITES2": "/data/CCBR_Pipeliner/db/PipeDB/lib/ALL.wgs.1000G_phase3.GRCh38.ncbi_remapper.20150424.shapeit2_indels.vcf.gz",
# "ALVIEWGENOME": "hg38",
"INDELSITES2": "/data/CCBR_Pipeliner/db/PipeDB/lib/ALL.wgs.1000G_phase3.GRCh38.ncbi_remapper.20150424.shapeit2_indels.vcf.gz",
"ALVIEWGENOME": "hg38",
"ONCOFUSEBUILD": "hg38",
# "EXONS": "/data/CCBR_Pipeliner/db/PipeDB/lib/hg38_exons.bed",
"EXONS": "/data/CCBR_Pipeliner/db/PipeDB/lib/hg38_exons.bed",
# "ANNDIR": "/data/CCBR_Pipeliner/db/PipeDB/AnnovarDB/",
# "tg_GS_INDELS": "/fdb/GATK_resource_bundle/hg38bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz",
# "tg_PHASE_INDELS": "/data/CCBR_Pipeliner/db/PipeDB/lib/ALL.wgs.1000G_phase3.GRCh38.ncbi_remapper.20150424.shapeit2_indels.vcf.gz",
# "SNP138": "/fdb/GATK_resource_bundle/hg38bundle/dbsnp_138.hg38.vcf.gz",
# "HAPMAP": "/fdb/GATK_resource_bundle/hg38bundle/hapmap_3.3.hg38.vcf.gz",
# "B1K": "/fdb/GATK_resource_bundle/hg38bundle/1000G_phase1.snps.high_confidence.hg38.vcf.gz",
# "OMNI": "/fdb/GATK_resource_bundle/hg38bundle/1000G_omni2.5.hg38.vcf.gz",
# "adapter.file": "/data/CCBR_Pipeliner/db/PipeDB/dev/TruSeq_and_nextera_adapters.ngsqc.dat",
"adapter.file": "/data/CCBR_Pipeliner/db/PipeDB/dev/TruSeq_and_nextera_adapters.ngsqc.dat",
"fastqc.adapters": "/data/CCBR_Pipeliner/db/PipeDB/dev/fastqc.adapters",
"trimmomatic.adapters": "/data/CCBR_Pipeliner/db/PipeDB/dev/adapters2.fa",
# "ORGANISM": "HUMAN",
# "AVIASET": "hg38",
"ORGANISM": "HUMAN",
"AVIASET": "hg38",
# "ADAPTER1": "AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC",
# "ADAPTER2": "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT",
# "nextera1": "CTGTCTCTTATACACATCTCCGAGCCCACGAGAC",
# "nextera2": "CTGTCTCTTATACACATCTGACGCTGCCGACGA",
# "DB29": "/data/CCBR_Pipeliner/db/PipeDB/snpEff_db/dbNSFP2.9.txt.gz",
# "SELECTDB": "SIFT_score,SIFT_pred,Polyphen2_HVAR_score,Polyphen2_HVAR_pred,LRT_score,LRT_pred,GERP++_RS,MutationAssessor_score,MutationAssessor_pred,1000Gp1_AF,1000Gp1_EUR_AF,ESP6500_EA_AF,ESP6500_AA_AF",
# "SNPEFF_GENOME": "GRCh38.82",
"SNPEFF_GENOME": "GRCh38.82",
"SNPEFF_CONFIG": "/usr/local/apps/snpEff/4.2/snpEff.config",
# "HAPMAP_DBNSFP": "/data/CCBR_Pipeliner/db/PipeDB/lib/snpEff_db/hapmap.bed",
# "REGULOMEDB": "/data/CCBR_Pipeliner/db/PipeDB/lib/snpEff_db/RegulomeDB.bed",
},
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