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From: Mark D. <dep...@br...> - 2011-12-12 16:16:17
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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 > > > This email and any files transmitted with it are confidential and intended > solely for the use of the addressee. If you are not the intended addressee, > then you have received this email in error and any use, dissemination, > forwarding, printing, or copying of this email is strictly prohibited. > Please notify us immediately of your unintended receipt by reply and then > delete this email and your reply. Cobb-Vantress, Inc. and its subsidiaries > and affiliates will not be held liable to any person resulting from the > unintended or unauthorized use of any information contained in this email > or as a result of any additions or deletions of information originally > contained in this email. > > > ------------------------------------------------------------------------------ > Learn Windows Azure Live! Tuesday, Dec 13, 2011 > Microsoft is holding a special Learn Windows Azure training event for > developers. It will provide a great way to learn Windows Azure and what it > provides. You can attend the event by watching it streamed LIVE online. > Learn more at http://p.sf.net/sfu/ms-windowsazure > _______________________________________________ > Samtools-help mailing list > Sam...@li... > https://lists.sourceforge.net/lists/listinfo/samtools-help > -- Mark A. DePristo, Ph.D. Associate Director, Medical and Population Genetics Analysis Broad Institute of MIT and Harvard dep...@br... ma...@de... |