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coverageCount - counting the coverage of mapped reads at each location on the

COVERAGECOUNT(1) User Commands COVERAGECOUNT(1)

NAME

coverageCount - counting the coverage of mapped reads at each location on the entire reference genome

DESCRIPTION

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.

USAGE

coverageCount [options] -i <input_file> -o <output_prefix>
Required arguments:
-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
Optional arguments:
-p
The input file contains paired-end reads.
--maxMOp <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.
July 2017 coverageCount 1.5.3+dfsg