Hi Petr, Thank you very much for your speedy reply. I opted to use multiple pipes to be on the safe side.
Thanks, Tommy On 04/10/2016 15:07:45, "Petr Danecek" <p...@sanger.ac.uk> wrote: >Hi, > >if I remember correctly the -i/-e options are applied before and >--max-af after subsetting. If unsure, or if a different behaviour is >needed, it is possible to stream multiple commands to make it explicit: > >$bt view -e .. -Ou | $bt view -s .. > >petr > > >On Tue, 2016-10-04 at 13:56 +0000, Tommy Carstensen wrote: >> To samtools-help, >> >> >> Is this list also for questions related to bcftools? >> >> >> The documentation for the tool PLINK lists the sequence in which >> command line flags are executed: >> https://www.cog-genomics.org/plink2/order >> >> >> Is there a similar page for bcftools? >> >> >> The reason I'm asking, is because I'm filtering out samples and then >> filtering based on AF. >> >> >> 1) Can I use either of the two methods below? >> 2) Will the AF be calculated for the filtered samples only? Or is the >> AF evaluated prior to sample filtering? >> >> >> bcftools view --exclude AF<0.1 >> bcftools view --max-af 0.1 >> >> >> Thank you very much. >> >> >> Tommy > > -- 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. ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
