NAME
coverageCount - counting the coverage of mapped reads at each location on the entire reference genome
DESCRIPTION
coverageCount Version 1.5.1
-
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:
--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.
coverageCount Version 1.5.1
-
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:
--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.