[REQUEST] samtools depth -aJ

[molly-hetheringtonrauth]

Feature Request

To help streamline our QC notebook, we can rely on the samtools coverage output to quickly check the coverage of the 69/70 deletion instead of opening up each bam file; however since this is a deletion region we need to update our samtools depth line to use the -J flag which includes reads with deletion in depth computation.

Solution

• In the SC2_ont_assembly.wdl, update the Bam_stats with samtools depth -aJ -o ~{sample_name}_~{index_1_id}_depth.txt ~{bam}. This output is already being transferred.
• In the SC2_illumina_pe_assembly.wdl update the bam_stats task with samtools depth -aJ -o ~{sample_name}_depth.txt ~{bam}. This outputs is already being transferred.

Upstream effects

None

Downstream effects

None

[molly-hetheringtonrauth]

check samtools versions; the current docker we are using doesn't seem to support "-J" flag.