Feature Request: Duphold Stats for Insertions

[jjfarrell]

It would be great that the Duphold stats be extended to insertions such as those generated by Manta. Duphold has been great for the QC of DEL and DUP FP variants.

[brentp]

what would be reported for insertions? duphold is mostly depth-based, but it could potentially extract other information.

[jjfarrell]

Here is one approach I think might work-At the insertion sites, the cigar should have an "I" in the read. So the depth of the insertion would be the number of reads with an "I" in the cigar string of the read at the insert site.