1 changed files with 7 additions and 2 deletions
+ 7
- 2
tasks/battenberg.wdl
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| cp ${normal_bam} ./${normal_id}.bam | cp ${normal_bam} ./${normal_id}.bam | ||||
| cp ${tumor_bam} ./${sample_id}.bam | cp ${tumor_bam} ./${sample_id}.bam | ||||
| samtools view -h ./${normal_id}.bam |sed 's/chr//g'|samtools view -bS -o ./${normal_id}.sorted.deduped.nochr.bam | |||||
| samtools view -h ./${sample_id}.bam |sed 's/chr//g'|samtools view -bS -o ./${sample_id}.sorted.deduped.nochr.bam | |||||
| samtools view -h -@ 16 -o ${normal_id}.sorted.deduped.sam ./${normal_id}.bam | |||||
| samtools view -h -@ 16 -o ${sample_id}.sorted.deduped.sam ./${sample_id}.bam | |||||
| sed -i 's/chr//g' ${normal_id}.sorted.deduped.sam | |||||
| sed -i 's/chr//g' ${sample_id}.sorted.deduped.sam | |||||
| samtools sort -@ 16 -o ${normal_id}.sorted.deduped.nochr.bam ${normal_id}.sorted.deduped.sam | |||||
| samtools sort -@ 16 -o ${sample_id}.sorted.deduped.nochr.bam ${sample_id}.sorted.deduped.sam | |||||
| >>> | >>> | ||||
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