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

# bdgcmp(1)

Calculate scores using certain method by comparing a bedGraph file from treatment and a file from control representing local bias

## NAME

bdgcmp - Calculate scores using certain method by comparing a bedGraph file from treatment and a file from control representing local bias

## SYNOPSIS

**bdgcmp** *\<-t TREATMENT.BEDGRAPH\> \<-c CONTROL.BEDGRAPH\> \<-o OUTPUT.BEDGRAPH\>* \[*-m METHOD*\]

## DESCRIPTION

Calculate scores using certain method by comparing a bedGraph file from treatment and a file from control representing local bias.

## OPTIONS

- **--version**

  show program's version number and exit

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

  Show this help message and exit.

- **-t** TFILE, **--tfile**=*TFILE*

  Required: Treatment bedGraph file, e.g. \*\_treat\_pileup.bdg from MACSv2

- **-c** CFILE, **--cfile**=*CFILE*

  Required: Control bedGraph file, e.g. \*\_control\_lambda.bdg from MACSv2

- **-o** OFILE, **--output**=*OFILE*

  Required: The output bedGraph file to write scores.

- **-m** METHOD, **--method**=*METHOD*

  Method to use while calculating a score in any bin by comparing treatment value and control value. Available choices are: ppois, substract, divide which represent Poisson Pvalue (**-log10**(pvalue) form) using control as lambda and treatment as observation, substraction from treatment, fold change which may be problematic if there are zero in control. Default option is ppois.