132 lines
3.7 KiB
Plaintext
132 lines
3.7 KiB
Plaintext
task rmdup_picard {
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String name
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String sorted_bam
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String output_dir
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String ref
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command <<<
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if [ ! -d ${output_dir}/fusion ];then
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mkdir ${output_dir}/fusion
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fi
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java -XX:+UseParallelGC -XX:ParallelGCThreads=8 -Xmx12G -jar $PICARD MarkDuplicates \
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I=${sorted_bam} \
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O=${output_dir}/alignment/${name}.picard.rmdup.bam \
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CREATE_INDEX=true \
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M=${output_dir}/alignment/${name}.picard.rmdup.metrics.txt \
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R=${ref}
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>>>
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output {
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String rmdup_bam = "${output_dir}/alignment/${name}.picard.rmdup.bam"
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}
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}
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task fusion_calling {
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String name
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String rmdup_bam
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String output_dir
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String ref
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String tumor_bamdst_depth
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command <<<
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if [ ! -d ${output_dir}/fusion ];then
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mkdir ${output_dir}/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 ${rmdup_bam} > ${output_dir}/fusion/${name}.discordants.bam
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# Extract the split-read alignments
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samtools view -h ${rmdup_bam} \
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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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> ${output_dir}/fusion/${name}.splitters.bam
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lumpyexpress \
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-B ${rmdup_bam} \
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-S ${output_dir}/fusion/${name}.splitters.bam \
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-D ${output_dir}/fusion/${name}.discordants.bam \
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-o ${output_dir}/fusion/${name}.fusion.raw.vcf
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python ~/project/pipeline/workflow/script/tools/vcf_filter.py \
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-i ${output_dir}/fusion/${name}.fusion.raw.vcf \
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-e 'INFO/PE[0] >1 && INFO/SR[0] > 4 ' \
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| svtyper -B ${rmdup_bam} -T ${ref} -o ${output_dir}/fusion/${name}.fusion.vcf
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table_annovar.pl \
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${output_dir}/fusion/${name}.fusion.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 ${output_dir}/fusion/${name}.fusion
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--remove
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filter_fusion.pl ${tumor_bamdst_depth} \
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${output_dir}/fusion/${name}.fusion.hg19_multianno.vcf \
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${output_dir}/fusion/${name}.fusion.hg19_multianno.filter.txt
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python ~/project/pipeline/workflow/script/tools/vcf_filter.py \
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-e 'INFO/SVTYPE == "DEL" | INFO/SVTYPE == "DUP" | INFO/SVTYPE == "INS" ' \
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-i ${output_dir}/fusion/${name}.fusion.hg19_multianno.vcf \
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-o ${output_dir}/fusion/${name}.longindel.hg19_multianno.vcf \
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>>>
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output {
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String vcf = "${output_dir}/fusion/${name}.fusion.vcf"
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}
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}
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workflow call_fusion {
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String name
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String sorted_bam
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String rmdup_bam
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String output_dir
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String ref
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Boolean umi
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String tumor_bamdst_depth
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if (umi) {
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call rmdup_picard {
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input:
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name=name,
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sorted_bam=sorted_bam,
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output_dir=output_dir,
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ref=ref
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}
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call fusion_calling as fusion_calling_umi {
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input:
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name=name,
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rmdup_bam=rmdup_picard.rmdup_bam,
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output_dir=output_dir,
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ref=ref,
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tumor_bamdst_depth=tumor_bamdst_depth
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}
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}
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if (!umi) {
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call fusion_calling as fusion_calling {
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input:
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name=name,
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rmdup_bam=rmdup_bam,
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output_dir=output_dir,
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ref=ref,
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tumor_bamdst_depth=tumor_bamdst_depth
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}
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}
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output {
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String fusion_vcf = "${output_dir}/fusion/${name}.fusion.vcf"
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}
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}
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