---
name: "macs2_bdgbroadcall"
section: "1"
platform: "linux"
package: "macs"
version: "2.2.7.1-6+b1"
release: "Debian 12 (Bookworm)"
platforms: ["linux"]
url: "https://new.carta.tech/macs2_bdgbroadcall"
---

# macs2\_bdgbroadcall(1)

Model-based Analysis for ChIP-Sequencing

## NAME

macs2\_bdgbroadcall - Model-based Analysis for ChIP-Sequencing

## DESCRIPTION

usage: macs2 bdgbroadcall \[-h\] **-i** IFILE \[-c CUTOFFPEAK\] \[-C CUTOFFLINK\]

- \[-l MINLEN\] \[-g LVL1MAXGAP\] \[-G LVL2MAXGAP\]

  \[--no-trackline\] \[--outdir OUTDIR\] (**-o** OFILE \| **--o-prefix** OPREFIX)

### options:

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

  show this help message and exit

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

  MACS score in bedGraph. REQUIRED

- **-c** CUTOFFPEAK, **--cutoff-peak** CUTOFFPEAK

  Cutoff for peaks depending on which method you used for score track. If the file contains qvalue scores from MACS2, score 2 means qvalue 0.01. DEFAULT: 2

- **-C** CUTOFFLINK, **--cutoff-link** CUTOFFLINK

  Cutoff for linking regions/low abundance regions depending on which method you used for score track. If the file contains qvalue scores from MACS2, score 1 means qvalue 0.1, and score 0.3 means qvalue 0.5. DEFAULT: 1

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

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

- **-g** LVL1MAXGAP, **--lvl1-max-gap** LVL1MAXGAP

  maximum gap between significant peaks, better to set it as tag size. DEFAULT: 30

- **-G** LVL2MAXGAP, **--lvl2-max-gap** LVL2MAXGAP

  maximum linking between significant peaks, better to set it as 4 times of d value. DEFAULT: 800

- **--no-trackline**

  Tells MACS not to include trackline with bedGraph files. The trackline is required by UCSC.

- **--outdir** OUTDIR

  If specified all output files will be written to that directory. Default: the current working directory

- **-o** OFILE, **--ofile** OFILE

  Output file name. Mutually exclusive with **--o-prefix**.

- **--o-prefix** OPREFIX

  Output file prefix. Mutually exclusive with **-o**/--ofile.