Feature Request: Duphold Stats for Insertions

brentp / duphold

don't get DUP'ed or DEL'ed by your putative SVs.

MIT License

100 stars 9 forks source link

Feature Request: Duphold Stats for Insertions #42

Open jjfarrell opened 3 years ago

jjfarrell commented 3 years ago

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 commented 3 years ago

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

jjfarrell commented 3 years ago

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.