---
name: "samtools.pl"
section: "1"
platform: "linux"
package: "samtools"
version: "1.21-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/samtools.pl"
---

# samtools.pl(1)

helper script for SAMtools

## NAME

samtools.pl - helper script for SAMtools

## SYNOPSIS

**samtools.pl** *\<command\>* \[*\<arguments\>*\]

## DESCRIPTION

helper script for SAMtools

- Command:

  varFilter     filtering SNPs and short indels

-

  pileup2fq     generate fastq from \`pileup **-c**'

-

  showALEN      print alignment length (ALEN) following CIGAR

## AUTHOR

THe software 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.