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 |
Technical Documentation Index |
GATK version 2.5-2-gdb4546e built at 2013/05/01 09:32:36.