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Missed deletion with SomaticIndelDetector

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


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?

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