Re: [Samtools-help] using mpileup with interval file

[Mark D. <dep...@br...>]

Hi Wes,

It doesn't seem like -l my.bed works with samtools mpileup but only
bcftools.  I would appreciate if a third-party would confirm / deny this
is.  It seems very expensive to me to run genome wide just to cut down to
exome intervals.

On Mon, Dec 12, 2011 at 11:13 AM, Barris, Wes
<Wes...@co...>wrote:

> Vladmir Makarov wrote on 2011-12-10:
>
> > Hello,
> >
> > I would like to generate pileup for certain intervals only. I know
> > about "-r" option
> >>> samtools mpileup -r 1:1000-2000 sorted.bam
> >
> > But list of intervals is too large to submit one by one. I tried
> > putting them to interval file 1:1000-2000 2:1000-2000 etc.
> >
> > and submit to mpileup.
> >
> >>> samtools mpileup -r targets.intervals  sorted.bam
> >
> > But had an error:
> >>> [mpileup] malformatted region or wrong seqname for 1-th input.
> >
> > Is there a way?
>
> The '-r' flag is for supplying a single region.  You want to put your
> regions (in BED format) and use the '-l' flag.
>
> --
> Wes Barris
>
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-- 

Mark A. DePristo, Ph.D.

Associate Director, Medical and Population Genetics Analysis

Broad Institute of MIT and Harvard

dep...@br...

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