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 -- James Bonfield (j...@sanger.ac.uk) The Sanger Institute, Hinxton, Cambs, CB10 1SA -- 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
