Filter out reads with wonky cigar strings.
- 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...
Guide Index |
Tool Documentation Index |
GATK version 3.1-1-g07a4bf8 built at 2014/03/18 07:00:36.