On Thu, Mar 17, 2016 at 09:16:49PM -0400, Michael Peng wrote: > samtools depth -b gene.bed a.bam > > It gives the result in a few seconds. The problem is samtools continue to > run for more than 10 mins.
This is a standard problem with BED vs region queries. We really ought to start a samtools FAQ. Region queries (eg -r chr1:1000-2000) use the indices while bed queries (-b) stream the entire data set and filter. If your region in the bed file is near the start of the file then it will give the results fast and then appear to hang while it streams past the rest of the file. It trips people up, myself included, because it's not guessable that the behaviour works this way. Logically speaking bed files could also be made to use the index, when it exists, in an intelligent manner. It's simply a matter of someone finding the time and inclination to do it. James -- James Bonfield ([email protected]) | Hora aderat briligi. Nunc et Slythia Tova | Plurima gyrabant gymbolitare vabo; A Staden Package developer: | Et Borogovorum mimzebant undique formae, https://sf.net/projects/staden/ | Momiferique omnes exgrabure Rathi. -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. ------------------------------------------------------------------------------ Transform Data into Opportunity. Accelerate data analysis in your applications with Intel Data Analytics Acceleration Library. Click to learn more. http://pubads.g.doubleclick.net/gampad/clk?id=278785351&iu=/4140 _______________________________________________ Samtools-help mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/samtools-help
