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.

samtools.pl 1.2                                   December 2015                                   SAMTOOLS.PL(1)