On Fri, May 04, 2018 at 11:05:32AM +0100, Jody Phelan wrote: > I am quite interested to know the results from the human chromosome. > Please let me know if there is anything I can do from my side.
I forgot to post it and it scrolled off my terminal now, but from memory it caused a slight increase in false negatives for indels, although nothing that significant. I could be wrong on that recollection though as I've been playing with all sorts of tweaks! The most recent test I did was setting any negative alignment score to something high on the grounds that it only happens with long runs of Ns and likely it's duff. This gave near identical results to the original method. I should add these tests were on realigned illumina data too, so I've no idea what the impacts would be on ONT, nor whether those statements would hold true on unrealigned data (eg as it comes from bwa), but bcftools indel isn't so hot in that situation anyway and it needs a lot of post-filtering to remove the huge false positive rate. I think the minor fluctuations on "common" data isn't so significant compared to the large amounts of aberrations we see overall, and the effect is far smaller than the impact of turning on/off the BAQ calculation. 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
