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tasks/depth.wdl
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| command <<< | command <<< | ||||
| /opt/conda/bin/samtools depth -b ${regions} ${raw_bam} > ${sample_id}.raw.depth | /opt/conda/bin/samtools depth -b ${regions} ${raw_bam} > ${sample_id}.raw.depth | ||||
| /opt/conda/bin/samtools depth -b ${regions} ${dedup_bam} > ${sample_id}.deduped.depth | |||||
| /opt/conda/bin/samtools depth -b ${regions} ${deduped_bam} > ${sample_id}.deduped.depth | |||||
| awk '{printf "%s:%i\t%i\n" , $1,$2,$3}' ${sample_id}.raw.depth | sort > ${sample_id}.raw.sorted.depth | awk '{printf "%s:%i\t%i\n" , $1,$2,$3}' ${sample_id}.raw.depth | sort > ${sample_id}.raw.sorted.depth | ||||
| awk '{printf "%s:%i\t%i\n" , $1,$2,$3}' ${sample_id}.deduped.depth | sort > ${sample_id}.deduped.sorted.depth | awk '{printf "%s:%i\t%i\n" , $1,$2,$3}' ${sample_id}.deduped.depth | sort > ${sample_id}.deduped.sorted.depth | ||||
| join -e NULL -a1 -j 1 -o 1.1,1.2,2.2 ${sample_id}.raw.sorted.depth ${sample_id}.deduped.sorted.depth > ${sample_id}.depth | join -e NULL -a1 -j 1 -o 1.1,1.2,2.2 ${sample_id}.raw.sorted.depth ${sample_id}.deduped.sorted.depth > ${sample_id}.depth |
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