For BAM in/out yes: inputthreads=<[1]> : input helper threads (for inputformat=bam only, default: 1) outputthreads=<[1]> : output helper threads (for outputformat=bam only, default: 1)
Keiran Raine Principal Bioinformatician Cancer Genome Project Wellcome Trust Sanger Institute k...@sanger.ac.uk Tel:+44 (0)1223 834244 Ext: 7703 Office: H104 > On 2 Aug 2016, at 12:57, Martin MOKREJŠ <mmokr...@gmail.com> wrote: > > Hi Keiran, > cool, does it run in multiple threads? "samtools clamd" runs in a single > thread in my hands, so this would certainly be a reason to change my pipeline. > > Keiran Raine wrote: >> Hi James, Martin, >> >> As James indicates BWA doesn't actually report the the correct MD tags as it >> changes all ambiguity and N positions to ACGT (by some reproducible method). >> >> I had requested addition of functionality to biobambam(2) to recalculate the >> MD if the read spanned any ambiguity/N positions: >> >> bamsort -h >> This is biobambam2 version 2.0.50. >> biobambam2 is distributed under version 3 of the GNU General Public License. >> ... >> calmdnm=<[0]> : calculate MD and NM aux fields (for >> coordinate sorted output only) >> calmdnmreference=<[]> : reference for calculating MD and NM aux >> fields (calmdnm=1 only) >> calmdnmrecompindetonly=<[0]> : only recalculate MD and NM in the presence >> of indeterminate bases (calmdnm=1 only) >> calmdnmwarnchange=<[0]> : warn when changing existing MD/NM fields >> (calmdnm=1 only) >> >> This gives you control over the warnings if that's what you specifically >> care about. > > Yes, otherwise I would just ignore them all. ;-) > > Martin -- 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.
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