Currently subsamplebam does not distinguish between orphaned (unpaired) and paired reads. But the ngs_mapper pipeline (specifically bam_to_depth and samtools mpileup only acknowledge paired reads. In this case, subsamplebam may subsample orphaned reads, giving less than the expected coverage depth from mpileup. Subsamplebam's behavior should be consistent with mpileup, and pick only paired reads unless otherwise specified.
Plan: My pull request will ignore unpaired reads by default. The "-A" flag (consistent with mpileup) will force it to consider unpaired reads.
necrolyte2
commented
9 years ago
Currently subsamplebam does not distinguish between orphaned (unpaired) and paired reads. But the ngs_mapper pipeline (specifically
bam_to_depthandsamtools mpileuponly acknowledge paired reads. In this case, subsamplebam may subsample orphaned reads, giving less than the expected coverage depth frommpileup. Subsamplebam's behavior should be consistent withmpileup, and pick only paired reads unless otherwise specified.Plan: My pull request will ignore unpaired reads by default. The "-A" flag (consistent with
mpileup) will force it to consider unpaired reads.