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SAMTOOLS.PL(1) User Commands SAMTOOLS.PL(1)

NAME

samtools.pl - helper script for SAMtools

SYNOPSIS

samtools.pl <command> [<arguments>]

DESCRIPTION

helper script for SAMtools

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.

December 2015 samtools.pl 1.2