BamUtil: findCigars
From Genome Analysis Wiki
Overview of the findCigars function of bamUtil
The findCigars option on the bamUtil executable outputs just the reads that contain any of the specified CIGAR operations.
Parameters
Required Parameters:
--in : the SAM/BAM file to be read
--out : the SAM/BAM file to be written
Optional Parameters:
--cinsert : output reads that contain insertions ('I').
--cdel : output reads that contain deletions ('D').
--cpad : output reads that contain pads ('P').
--cskip : output reads that contain skips ('N').
--chardClip : output reads that contain hard clips ('H').
--csoftClip : output reads that contain soft clips ('S').
--nonM : output reads that contain any non match/mismatch (anything other than 'M', '=', 'X')
--noeof : do not expect an EOF block on a bam file.
--params : print the parameter settings
Usage
./bam findCigars --in <inputFile> --out <outputFile.sam/bam/ubam (ubam is uncompressed bam)> [--cinsert] [--cdel] [--cpad] [--cskip] [--chardClip] [--csoftClip] [--nonM] [--noeof] [--params]
Return Value
Returns the SamStatus for the reads/writes.
Example Output
Number of records read = 10 Number of records written = 1
