375 lines
12 KiB
Plaintext
375 lines
12 KiB
Plaintext
#create project directory
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task create_dir {
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String workdir
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command <<<
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if [ ! -d ${workdir}];then
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mkdir -p ${workdir}/log
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fi
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>>>
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}
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task mutation_calling {
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String name
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String tumor_pileup
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String normal_pileup
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String outputDir
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command <<<
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if [ ! -d ${outputDir}/mutation ];then
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mkdir ${outputDir}/mutation
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fi
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java -jar $VARSCAN somatic ${tumor_pileup} ${normal_pileup} \
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--output-snp ${outputDir}/mutation/${name}.snp.vcf \
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--output-indel ${outputDir}/mutation/${name}.indel.vcf \
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--min-var-freq 0.01 \
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--min-freq-for-hom 0.9 \
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--somatic-p-value 0.05 \
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--output-vcf 1 \
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--min-avg-qual 20 \
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--min-coverage-normal 10 \
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--min-coverage-tumor 30 --min-reads2 3
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java -jar $VARSCAN processSomatic \
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${outputDir}/mutation/${name}.snp.vcf \
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--min-tumor-freq 0.01 \
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--max-normal-freq 0.01 \
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--p-value 0.05
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java -jar $VARSCAN processSomatic \
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${outputDir}/mutation/${name}.indel.vcf \
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--min-tumor-freq 0.01 \
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--max-normal-freq 0.01 \
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--p-value 0.05
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java -jar $GATK MergeVcfs \
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-I ${outputDir}/mutation/${name}.snp.Somatic.hc.vcf \
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-I ${outputDir}/mutation/${name}.indel.Somatic.hc.vcf \
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-O ${outputDir}/mutation/${name}.snp.indel.Somatic.hc.vcf \
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-D /dataseq/jmdna/database/genome/hg19/hg19.dict
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java -jar $GATK MergeVcfs \
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-I ${outputDir}/mutation/${name}.snp.Germline.vcf \
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-I ${outputDir}/mutation/${name}.indel.Germline.vcf \
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-O ${outputDir}/mutation/${name}.snp.indel.Germline.vcf \
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-D /dataseq/jmdna/database/genome/hg19/hg19.dict
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java -jar $GATK MergeVcfs \
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-I ${outputDir}/mutation/${name}.snp.LOH.hc.vcf \
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-I ${outputDir}/mutation/${name}.indel.LOH.hc.vcf \
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-O ${outputDir}/mutation/${name}.snp.indel.LOH.hc.vcf \
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-D /dataseq/jmdna/database/genome/hg19/hg19.dict
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>>>
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output {
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String somatic_hc_vcf = "${outputDir}/mutation/${name}.snp.indel.Somatic.hc.vcf"
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String germline_vcf="${outputDir}/mutation/${name}.snp.indel.Germline.vcf"
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String loh_hc_vcf="${outputDir}/mutation/${name}.snp.indel.LOH.hc.vcf"
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}
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}
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task annovar {
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String name
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String outputDir
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String ref
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String somatic_hc_vcf
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String germline_vcf
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String loh_hc_vcf
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String rmdupBam
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command <<<
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if [ ! -d ${outputDir}/mutation ];then
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mkdir ${outputDir}/mutation
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fi
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table_annovar.pl \
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${somatic_hc_vcf} \
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/dataseq/jmdna/software/annovar/humandb/ \
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-buildver hg19 -nastring . -vcfinput -remove -otherinfo \
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-protocol refGene,avsnp150,cosmic91,clinvar_20220320,1000g2015aug_all,1000g2015aug_eas,esp6500siv2_all,exac03nontcga,gnomad_genome,dbnsfp35c,cytoBand \
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-argument '-splicing_threshold 2 -hgvs',,,,,,,,,, \
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--intronhgvs 50 \
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-operation g,f,f,f,f,f,f,f,f,f,r \
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--outfile ${outputDir}/mutation/${name}.snp.indel.Somatic.anno
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table_annovar.pl \
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${germline_vcf} \
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/dataseq/jmdna/software/annovar/humandb/ \
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-buildver hg19 -nastring . -vcfinput -remove -otherinfo \
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-protocol refGene,avsnp150,cosmic91,clinvar_20220320,1000g2015aug_all,1000g2015aug_eas,esp6500siv2_all,exac03nontcga,gnomad_genome,dbnsfp35c,cytoBand \
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-argument '-splicing_threshold 2 -hgvs',,,,,,,,,, \
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--intronhgvs 50 \
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-operation g,f,f,f,f,f,f,f,f,f,r \
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--outfile ${outputDir}/mutation/${name}.snp.indel.Germline.anno
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table_annovar.pl \
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${loh_hc_vcf} \
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/dataseq/jmdna/software/annovar/humandb/ \
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-buildver hg19 -nastring . -vcfinput -remove -otherinfo \
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-protocol refGene,avsnp150,cosmic91,clinvar_20220320,1000g2015aug_all,1000g2015aug_eas,esp6500siv2_all,exac03nontcga,gnomad_genome,dbnsfp35c,cytoBand \
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-argument '-splicing_threshold 2 -hgvs',,,,,,,,,, \
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--intronhgvs 50 \
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-operation g,f,f,f,f,f,f,f,f,f,r \
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--outfile ${outputDir}/mutation/${name}.snp.indel.LOH.anno
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java -jar /dataseq/jmdna/software/GenomeAnalysisTK.3.7.jar -T VariantAnnotator \
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-R ${ref} \
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-I ${rmdupBam} \
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-V ${somatic_hc_vcf} \
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-o ${outputDir}/mutation/${name}.TandemRepeatAnnotator.vcf \
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--annotation TandemRepeatAnnotator
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grep -v "^##" ${outputDir}/mutation/${name}.TandemRepeatAnnotator.vcf \
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|cut -f8| paste ${outputDir}/mutation/${name}.snp.indel.Somatic.anno.hg19_multianno.txt - \
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> ${outputDir}/mutation/${name}.snp.indel.Somatic.annoall.hg19_multianno.txt
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>>>
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output {
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String somatic_anno = "${outputDir}/mutation/${name}.snp.indel.Somatic.anno.hg19_multianno.txt"
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String germline_anno = "${outputDir}/mutation/${name}.snp.indel.Germline.anno.hg19_multianno.txt"
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String somatic_all_anno = "${outputDir}/mutation/${name}.snp.indel.Somatic.annoall.hg19_multianno.txt"
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}
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}
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task tmb {
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String codesDir
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String name
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String outputDir
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String somatic_anno
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command <<<
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perl ${codesDir}/tmb.pl ${outputDir} ${name}
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>>>
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output {
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String tmb="${outputDir}/mutation/${name}.tmb.txt"
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}
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}
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task fusion {
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String name
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String ref
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String codesDir
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String outputDir
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String rmdupBam
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String cancer
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String project
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String tumor_bamdst_depth
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command <<<
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if [ ! -d ${outputDir}/fusion ];then
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mkdir ${outputDir}/fusion
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fi
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# Extract the discordant paired-end alignments.
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samtools view -b -F 1294 ${rmdupBam} > ${outputDir}/fusion/${name}.discordants.bam
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# Extract the split-read alignments
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samtools view -h ${rmdupBam} \
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| /dataseq/jmdna/software/lumpy-sv/scripts/extractSplitReads_BwaMem -i stdin \
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| samtools view -Sb - \
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> ${outputDir}/fusion/${name}.splitters.bam
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lumpyexpress \
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-B ${rmdupBam} \
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-S ${outputDir}/fusion/${name}.splitters.bam \
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-D ${outputDir}/fusion/${name}.discordants.bam \
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-o ${outputDir}/fusion/${name}.fusion.vcf
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perl ${codesDir}/fusion.filter.pl ${outputDir}/fusion/${name}.fusion.vcf ${outputDir}/fusion/${name}.fusion.filter.vcf
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svtyper \
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-B ${rmdupBam} \
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-i ${outputDir}/fusion/${name}.fusion.filter.vcf \
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-T ${ref} \
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-o ${outputDir}/fusion/${name}.fusion.gt.vcf
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table_annovar.pl \
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${outputDir}/fusion/${name}.fusion.gt.vcf \
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/dataseq/jmdna/software/annovar/humandb/ \
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-buildver hg19 -nastring . -vcfinput -remove -otherinfo \
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-protocol refGene \
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-operation g \
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--outfile ${outputDir}/fusion/${name}.fusion
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perl ${codesDir}/fusion.reanno.pl ${tumor_bamdst_depth} ${outputDir} ${name}
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perl /home/jm001/test_duantao/database_update/codes/682/fusion_targetTherapy.pl ${codesDir} ${name} ${outputDir} ${project} ${cancer}
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>>>
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output {
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String fusion = "${outputDir}/fusion/${name}.fusion.pos.txt"
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}
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}
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task tumor_content {
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String name
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String tumor_pileup
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String normal_pileup
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String ref
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String outputDir
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String codesDir
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String gc_wiggle = "/dataseq/jmdna/codes/pancancer_controlsample/hg19.gc200Base.txt.gz"
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command <<<
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sequenza-utils bam2seqz \
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-p -gc ${gc_wiggle} \
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-F ${ref} \
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-n ${normal_pileup} \
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-t ${tumor_pileup} \
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| gzip > ${outputDir}/qc/target_${name}.200base.seqz.gz
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sequenza-utils seqz_binning -w 200 -s ${outputDir}/qc/target_${name}.200base.seqz.gz \
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| gzip > ${outputDir}/qc/target_${name}.200base.small.seqz.gz
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Rscript ${codesDir}/sequenza.R ${name} ${outputDir}/qc/target_${name}.200base.small.seqz.gz ${outputDir}/qc/sequenza || echo "sequenza failed!"
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>>>
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output {
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String purity = "${outputDir}/qc/sequenza/${name}_CP_contours.pdf"
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}
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}
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task cnvkit {
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String tumor
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String normal
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String tumor_rmdupBam
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String normal_rmdupBam
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String ref
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String bed
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String outputDir
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String cancer
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String codesDir
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String project
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String accessBed = "/dataseq/jmdna/software/cnvkit-0.9.7/data/access-5k-mappable.hg19.bed"
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String annotateGene = "/dataseq/jmdna/software/cnvkit-0.9.7/data/refFlat.txt"
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command <<<
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if [ ! -d ${outputDir}/cnvkit ];then
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mkdir ${outputDir}/cnvkit
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fi
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cnvkit.py batch \
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${tumor_rmdupBam} \
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--normal ${normal_rmdupBam} \
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--targets ${bed} \
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--fasta ${ref} \
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--access ${accessBed} \
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--output-reference ${outputDir}/cnvkit/${normal}_reference.cnn \
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--annotate ${annotateGene} \
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--drop-low-coverage --scatter --output-dir ${outputDir}/cnvkit
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cnvkit.py scatter \
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${outputDir}/cnvkit/${tumor}.rmdup.cnr -s ${outputDir}/cnvkit/${tumor}.rmdup.cns \
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--y-max 3 --y-min -3 \
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--title ${tumor}.cns \
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-o ${outputDir}/cnvkit/${tumor}.cnv.png
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perl ${codesDir}/log2_cn.pl ${outputDir}/cnvkit/${tumor}.rmdup.cns ${outputDir}/cnvkit/${tumor}.rmdup.cns.cn
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perl /home/jm001/test_duantao/database_update/codes/682/cnv_targetTherapy.pl ${codesDir} ${tumor} ${outputDir} ${project} ${cancer}
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>>>
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output {
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String cnv = "${outputDir}/cnvkit/${tumor}.rmdup.cns"
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}
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}
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task chemo {
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String codesDir
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String outputDir
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String project
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String normal
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String rmdupBam
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command <<<
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if [ ! -d ${outputDir}/chemo ];then
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mkdir ${outputDir}/chemo
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fi
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${codesDir}/chemo/chemo_panel.py -p ${project} -o ${outputDir} --n ${normal}
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>>>
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}
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task msi {
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String bed
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String name
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String outputDir
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String tumor_rmdupBam
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String normal_rmdupBam
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command <<<
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if [ ! -d ${outputDir}/msi ];then
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mkdir ${outputDir}/msi
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fi
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msisensor2 msi -d /dataseq/jmdna/software/msisensor2/hg19.microsatellites.list \
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-n ${normal_rmdupBam} \
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-t ${tumor_rmdupBam} \
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-e ${bed} -b 10 -o ${outputDir}/msi/${name}.msi
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>>>
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output {
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String target="${outputDir}/MSI/${name}.msi"
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}
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}
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task hla {
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String inputDir
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String outputDir
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String normal
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command <<<
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if [ ! -d ${outputDir}/neoantigen ];then
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mkdir -p ${outputDir}/neoantigen/HLA
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fi
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razers3 -tc 10 -i 95 -m 1 -dr 0 \
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-o ${outputDir}/neoantigen/HLA/fished_1.bam /dataseq/jmdna/software/OptiType-1.3.5/data/hla_reference_dna.fasta \
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${inputDir}/*_${normal}_*1.fq.gz
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samtools bam2fq ${outputDir}/neoantigen/HLA/fished_1.bam > ${outputDir}/neoantigen/HLA/${normal}_1_fished.fastq
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rm ${outputDir}/neoantigen/HLA/fished_1.bam
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razers3 -tc 10 -i 95 -m 1 -dr 0 \
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-o ${outputDir}/neoantigen/HLA/fished_2.bam /dataseq/jmdna/software/OptiType-1.3.5/data/hla_reference_dna.fasta \
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${inputDir}/*_${normal}_*2.fq.gz
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samtools bam2fq ${outputDir}/neoantigen/HLA/fished_2.bam > ${outputDir}/neoantigen/HLA/${normal}_2_fished.fastq
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rm ${outputDir}/neoantigen/HLA/fished_2.bam
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/dataseq/jmdna/software/OptiType-1.3.5/OptiTypePipeline.py \
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-i ${outputDir}/neoantigen/HLA/${normal}_1_fished.fastq ${outputDir}/neoantigen/HLA/${normal}_2_fished.fastq \
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--dna -v --prefix ${normal} -o ${outputDir}/neoantigen/HLA/
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>>>
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output {
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String hla = "${outputDir}/neoantigen/HLA/${normal}_result.tsv"
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}
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}
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task neoantigen {
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String codesDir
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String outputDir
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String name
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String normal
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String somatic_hc_vcf
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String hla
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command <<<
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sh /home/jm001/test_duantao/database_update/test_project/20230814_test/predict_neoantigen.sh ${outputDir} ${name} ${name} ${codesDir}
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>>>
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output {
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String neoantigen = "${outputDir}/neoantigen/MHC_Class_I/${name}.all_epitopes.netchop.txt"
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}
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}
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