On Wed, Nov 26, 2014 at 3:49 AM, Charles Plessy <ple...@debian.org> wrote:
> > in recent versions of samtools, the mpileup command has a new option > to specify the coverage at run time. > > Would it be fine to drop our patch that was raising the default coverage > cap > from 8,000 to 1,000,000 ? If yes, do you think we need to mention it as a > NEWS > entry ? > > Hi Charles, I think we still need the patch. samtools depth doesn't support the -d flag. $ samtools --version samtools 1.1 Using htslib 1.1 Copyright (C) 2014 Genome Research Ltd. $ samtools depth Usage: samtools depth [options] in1.bam [in2.bam [...]] Options: -b <bed> list of positions or regions -f <list> list of input BAM filenames, one per line [null] -l <int> minQLen -q <int> base quality threshold -Q <int> mapping quality threshold -r <chr:from-to> region $ ./samtools mpileup Usage: samtools mpileup [options] in1.bam [in2.bam [...]] Input options: ... -d, --max-depth INT max per-BAM depth; avoids excessive memory usage [250] ... Best -Dominique
