Showing docs for version 3.7-0
BadCigarFilter
Filter out reads with wonky CIGAR strings
Category
Read Filters
Overview
This read filter will filter out the following cases:
- different length and cigar length
- Hard/Soft clips in the middle of the cigar
- starting with deletions (with or without preceding clips)
- ending in deletions (with or without follow-up clips)
- fully hard or soft clipped
- consecutive indels in the cigar (II, DD, ID or DI)
Usage example
Enable the bad cigar filter
java -jar GenomeAnalysisTk.jar \
-T ToolName \
-R reference.fasta \
-I input.bam \
-o output.file \
-rf BadCigar