* change a default parameter
use warnings;
use Getopt::Std;
use warnings;
use Getopt::Std;
&usage if (@ARGV < 1);
my $command = shift(@ARGV);
&usage if (@ARGV < 1);
my $command = shift(@ARGV);
- my %opts = (d=>3, D=>255, Q=>40, G=>50, l=>10);
+ my %opts = (d=>3, D=>255, Q=>25, G=>50, l=>10);
getopts('d:D:Q:G:l:', \%opts);
die(qq/
Usage: samtools.pl pileup2fq [options] <in.cns-pileup>
getopts('d:D:Q:G:l:', \%opts);
die(qq/
Usage: samtools.pl pileup2fq [options] <in.cns-pileup>
+Program: samtools.pl (helper script for SAMtools)
+Version: $version
+Contact: Heng Li <lh3\@sanger.ac.uk>\n
Usage: samtools.pl <command> [<arguments>]\n
Command: indelFilter filter indels generated by `pileup -c'
snpFilter filter SNPs generated by `pileup -c'
Usage: samtools.pl <command> [<arguments>]\n
Command: indelFilter filter indels generated by `pileup -c'
snpFilter filter SNPs generated by `pileup -c'