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.