coverageCount - counting the coverage of mapped reads at each location on the
entire reference genome
This program calculates the coverage of mapped reads at each location on
the reference genome. It generates a binary file for each chromosome by
concatenating the coverage levels as 4-bytes integer numbers.
coverageCount [options] -i
- -i <string>
- Name of input file in SAM or BAM format.
- -o <string>
- Prefix of the output files. Each output file contains
Four-byte integer numbers
- The input file contains paired-end reads.
<int> Maximum number of 'M' operations allowed in a CIGAR string.
- 10 by default. Both 'X' and '=' are treated as 'M' and
adjacent 'M' operations are merged in the CIGAR string.