1 changed files with 2 additions and 2 deletions
+ 2
- 2
tasks/battenberg.wdl
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| set -e | set -e | ||||
| 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 ./${normal_id}.bam |sed 's/chr//g'|samtools view -bS > ./${normal_id}.sorted.deduped.nochr.bam | |||||
| samtools view -h ./${sample_id}.bam |sed 's/chr//g'|samtools view -bS > ./${sample_id}.sorted.deduped.nochr.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 index ./${normal_id}.sorted.deduped.nochr.bam | samtools index ./${normal_id}.sorted.deduped.nochr.bam |
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