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tasks/depth.wdl
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| @@ -10,10 +10,10 @@ task depth { | |||
| String disk_size | |||
| command <<< | |||
| /opt/conda/bin/samtools depth -b ${regions} ${raw_bam} > ${sample_id}.raw.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}.deduped.depth | sort > ${sample_id}.deduped.sorted.depth | |||
| /opt/conda/bin/samtools depth -a -b ${regions} ${raw_bam} > ${sample_id}.raw.depth | |||
| /opt/conda/bin/samtools depth -a -b ${regions} ${deduped_bam} > ${sample_id}.deduped.depth | |||
| sort -k1,1V -k2,2n ${sample_id}.raw.depth | awk '{printf "%s:%i\t%i\n" , $1,$2,$3}' > ${sample_id}.raw.sorted.depth | |||
| sort -k1,1V -k2,2n ${sample_id}.deduped.depth | awk '{printf "%s:%i\t%i\n" , $1,$2,$3}' > ${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 | |||
| >>> | |||
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