---
name: "coverageCount"
section: "1"
platform: "linux"
package: "subread"
version: "1.5.1+dfsg-4"
release: "Debian 9 (Stretch)"
platforms: ["linux"]
url: "https://new.carta.tech/coverageCount"
---

# coverageCount(1)

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

## 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.