coverageCount1
Counting the coverage of mapped reads at each location on the entire reference genome
Overview
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.