---
name: "maq.pl"
section: "1"
platform: "linux"
package: "maq"
version: "0.7.1-10"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/maq.pl"
---

# maq.pl(1)

helper script for maq

## NAME

maq.pl - helper script for maq

## SYNOPSIS

**maq.pl** *\<command\>* \[*options*\] *\<input\>* \[...\]

## DESCRIPTION

helper script for maq

Version: 0.4.7

## OPTIONS.

- *easyrun*

  simple pipeline for small dataset

- *demo*

  demonstration of maq functionalities (for SE only)

- *SNPfilter*

  filter SNPs

- *statmap*

  extract statistics from the error output of 'maq map'

- *chrpt2snp*

  convert dbSNP's chr\_rpt file to .snp file

- *ucsc2snp*

  convert UCSC's SNP dump to .snp file

- *fastq2bfq*

  convert fastq in batch

- *cat2pair*

  convert paired end reads format

- *sv*

  call structural variations

- *indelpe*

  post-processing indelpe output

## AUTHOR

The program was written by Heng Li \<lh3@sanger.ac.uk\>.

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.