James Bonfield wrote: > On Tue, Aug 02, 2016 at 01:44:01PM +0200, Martin MOKREJ? wrote: >>> The warnings are there because it is correcting the aligner output. >>> The proper fix is to fix the aligners to produce the correct MD in the >>> first place, not to break calmd to be buggy in the same manner. >> >> Hmm, but bwa mem did not introduce the MD: tag, see the lines from >> >> samtools view mysample-PB.bam | grep >> HWI-xxxxx:xxx:xxxxxxxxx:2:1101:1110:65038 >> >> in a previous email. > > Ok fair enough, consider my maligning of the aligner rescinded!
Pardon me? I am not a native speaker. ;-) > > However the point is still valid; somewhere some tool wrote incorrect > MD tags. It is not appropriate to make Samtools gloss over these > errors, or worse, change the algorithm to compute things in the same > broken manner. "samtools calmd" is the first tool in my pipeline writing out the MD: tag, but as it turned out this is more about NM: tag being mistaken, and that was bwa mem's job. (I don't even know how to tell bwa mem to output also MD: tag at the first sweep. > > It may be worth studying the @PG lines to figure out where the duff MD > tags came from and send in a bug report. > >> So, I still think "samtools calmd" could be less verbose. > > It's a valid warning, but maybe there should be a silent mode. Most people use bwa mem it seems, and I tried to use stampy on top of it to improve mapping but I am not certain it is a good idea if I use GRCH38DH due to the alt locations which would need to be supported in the stampy code. I assume it is not coping with alt loci, and I do not have the alt file because bwa mem is said to infer alternative mapping from the reference contignames containing _alt, _unknown, _random, whatever. > However with non-broken data you'll find it is very quiet so > collectively I think the effort should be placed at fixing the > tool that produced data. :-) Indeed, join https://github.com/lh3/bwa/issues/82 . ------------------------------------------------------------------------------ _______________________________________________ Samtools-help mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/samtools-help
