You are right, for single-sample calling filtering on IMF and IDV should do the same thing as -F, -m. The difference would be only in multisample calling, provided -p is not given.
The only other options to play with are the gap open penalty etc, but I doubt it will improve things dramatically. Petr On Tue, 2018-02-06 at 09:39 +0000, James Bonfield wrote: > On Tue, Feb 06, 2018 at 10:13:06AM +0100, Petr Danecek wrote: > > > > It is probably the default mpileup -F and -m options are way too > > small. > > Are they the values which ultimately end up in IMF and IDV? If so, > setting them low is OK provided they are then used for computing QUAL > and/or a recommendation of post-filtering or even default filtering > via PASS. > > This is like GATK --stand_emit_conf and --stand_call_conf where low > quality calls are written to the VCF but by default are not > considered > as passes. It allows the user the ability to adjust the threshold > post-calling without needing to start again from scratch. > > Do you have any other parameters you recommend? I think we could do > with a HOWTO on this too. > > James > -- The Wellcome 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
