---
name: "bdgpeakcall"
section: "1"
platform: "linux"
package: "macs"
version: "2.0.9.1-1"
release: "Debian 8 (Jessie)"
platforms: ["linux"]
url: "https://new.carta.tech/bdgpeakcall"
---

# bdgpeakcall(1)

Naive call peaks from a single bedGraph track for scores

## NAME

bdgpeakcall - Naive call peaks from a single bedGraph track for scores

## SYNOPSIS

**bdgpeakcall** *\<-i bedGraph\>* \[*-c CUTOFF*\] \[*-l MIN*\] \[*-g MAX*\] \[*-o PREFIX*\]

## DESCRIPTION

Call peaks from MACS pvalue or qscore score bedGraph output, with customized settings. Output encodePeak format peaks, combining peak boundaries, peak summits.

## OPTIONS

- **--version**

  show program's version number and exit

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

  Show this help message and exit.

- **-i** IFILE, **--ifile**=*IFILE*

  MACS pvalue score bedGraph

- **-c** CUTOFF, **--cutoff**=*CUTOFF*

  Cutoff depends on which method you used for score track. If the file contains pvalue scores from MACS2, score 5 means pvalue 1e-5. DEFAULT: 5

- **-l** MINLEN, **--min-length**=*MINLEN*

  minimum length of peak, better to set it as d value. DEFAULT: 200

- **-g** MAXGAP, **--max-gap**=*MAXGAP*

  maximum gap between significant points in a peak, better to set it as tag size. DEFAULT: 30

- **-o** OPREFIX, **--o-prefix**=*OPREFIX*

  output file prefix, DEFAULT: peak