4.9. jsa.hts.countReads: Count reads from bam files¶

4.9.1. Synopsis¶

jsa.hts.countReads: Count the number of reads in some regions from a sorted, indexed bam file

4.9.2. Usage¶

jsa.hts.countReads [options]

4.9.3. Options¶

--bamFile=s Name of the bam file (REQUIRED)

--bedFile=s Name of the regions file in bed format (REQUIRED)

--output=s Name of output file, - for from standard out. (default=’-‘)

--flanking=i Size of the flanking regions, effectively expand the region by flanking (default=‘0’)

--qual=i Minimum quality (default=‘0’)

--filterBits=i

Filter reads based on flag. Common values:

0 no filter 256 exclude secondary alignment 1024 exclude PCR/optical duplicates 2048 exclude supplementary alignments

(default=‘0’)

--contained Count reads contained in the region (default=’false’)

--overlap Count number of read overlap with the region (default=’false’)

--span Count reads span the region (default=’false’)

--help Display this usage and exit (default=’false’)