Should depth/quality plots include anomalous read pairs?

[averagehat]

Currently the bam_to_qualdepth module uses the bdq.mpileup method to generate the depth+quality plots. By default, samtools mpileup ignores "orphaned" or "anomalous" reads (those are paired reads where the mate is not paired). Should we add the "-A" flag to the command to include the anomalous reads?

[necrolyte2]

@mmelendrez will have to answer that one

I could see it going either way as the bqd.mpileup is a duplicate function almost to the samtools.mpileup

Migration is still needed to move any existing code using bqd.mpileup over to samtools.mpileup.
Regardless, we should probably decide if we should be using the -A flag as neither function use it currently.

[averagehat]

This will be a config option with the default set to "no orphans"

[necrolyte2]

Should we make it so that it makes more sense such as
include_orphans: yes|true|no|false and defaults to no

[averagehat]

yes

[averagehat]

I don't think this is really a filter issue, this is a flag that we might add to the base caller/plotting scripts. Dropping the filter milestone.