Bug Bulletin: The recent 3.2 release fixes many issues. If you run into a problem, please try the latest version before posting a bug report, as your problem may already have been solved.

Missed deletion with SomaticIndelDetector

travisbickle34travisbickle34 Posts: 9Member
edited August 2013 in Ask the GATK team

Hi,

I am trying to explain a missed INDEL call with SomaticIndelDetector. It is a pretty obvious call. There are plenty of reads to support it, qualities are good etc. Plus I am running with very permissive settings (--filter_expressions T_COV<5||N_COV<5||T_INDEL_F<0.02||T_INDEL_CF<0.1).

No matter what I try though, the caller does not catch the deletion. Is there any way to get further explanaion for something like this or do I just have to put it in the idiosyncrasy bracket?

Post edited by travisbickle34 on

Best Answer

Answers

Sign In or Register to comment.