And no, sorry, I am afraid we do not have this documented. petr
On Tue, 2016-10-04 at 16:07 +0200, Petr Danecek 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
