Missed deletion with SomaticIndelDetector
Posted in Ask the GATK team | Last updated on 2013-08-28 20:38:22


Comments (2)

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?


Return to top Comment on this article in the forum