---
name: "cnvkit-coverage"
section: "1"
platform: "linux"
package: "cnvkit"
version: "0.9.12-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/cnvkit-coverage"
---

# cnvkit-coverage(1)

Calculate coverage in the given regions from BAM read depths.

## NAME

cnvkit\_coverage - Calculate coverage in the given regions from BAM read depths.

## DESCRIPTION

usage: cnvkit.py coverage \[-h\] \[-f FILENAME\] \[-c\] \[-q MIN\_MAPQ\] \[-o FILENAME\]

- \[-p \[PROCESSES\]\]

  bam\_file interval

### positional arguments:

- bam\_file

  Mapped sequence reads (.bam)

- interval

  Intervals (.bed or .list)

### options:

- **-h**, **--help**

  show this help message and exit

- **-f** FILENAME, **--fasta** FILENAME

  Reference genome, FASTA format (e.g. UCSC hg19.fa)

- **-c**, **--count**

  Get read depths by counting read midpoints within each bin. (An alternative algorithm).

- **-q** MIN\_MAPQ, **--min-mapq** MIN\_MAPQ

  Minimum mapping quality score (phred scale 0-60) to count a read for coverage depth. \[Default: 0\]

- **-o** FILENAME, **--output** FILENAME

  Output file name.

- **-p** \[PROCESSES\], **--processes** \[PROCESSES\]

  Number of subprocesses to calculate coverage in parallel. Without an argument, use the maximum number of available CPUs. \[Default: use 1 process\]