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 <[email protected]>.

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