table of contents
- stretch 1.5.1+dfsg-4
COVERAGECOUNT(1) | User Commands | COVERAGECOUNT(1) |
NAME¶
coverageCount - counting the coverage of mapped reads at each location on the entire reference genomeDESCRIPTION¶
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.
December 2016 | coverageCount 1.5.1+dfsg-4 |