Filter out reads with wonky cigar strings.

Category Read Filters


- No reads with Hard/Soft clips in the middle of the cigar - No reads starting with deletions (with or without preceding clips) - No reads ending in deletions (with or without follow-up clips) - No reads that are fully hard or soft clipped - No reads that have consecutive indels in the cigar (II, DD, ID or DI) ps: apparently an empty cigar is okay...

See also Guide Index | Tool Documentation Index | Support Forum

GATK version 3.2-2-gec30cee built at 2014/09/12 22:29:29. GTD: NA