---
name: "covtobed"
section: "1"
platform: "linux"
package: "covtobed"
version: "1.3.5+dfsg-2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/covtobed"
---

# covtobed(1)

convert the coverage track from a BAM file into a BED file

## NAME

covtobed - convert the coverage track from a BAM file into a BED file

## SYNOPSIS

**covtobed** \[*options*\] \[*BAM*\]...

## DESCRIPTION

Computes coverage from alignments

## OPTIONS

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

  show this help message and exit

- **--version**

  show program's version number and exit

- **--physical-coverage**

  compute physical coverage (needs paired alignments in input)

- **-q** MINQ, **--min-mapq**=*MINQ*

  skip alignments whose mapping quality is less than MINQ (default: 0)

- **-m** MINCOV, **--min-cov**=*MINCOV*

  print BED feature only if the coverage is bigger than (or equal to) MINCOV (default: 0)

- **-x** MAXCOV, **--max-cov**=*MAXCOV*

  print BED feature only if the coverage is lower than MAXCOV (default: 100000)

- **-l** MINLEN, **--min-len**=*MINLEN*

  print BED feature only if its length is bigger (or equal to) than MINLELN (default: 1)

- **-d**, **--discard-invalid-alignments**

  skip duplicates, failed QC, and non primary alignment, minq\>0 (or user-defined if higher) (default: 0)

- **--output-strands**

  output coverage and stats separately for each strand

- **--format**=*CHOICE*

  output format