Re: [Samtools-help] samtools calmd behavior and MD tag

Keiran Raine wrote: > >> On 2 Aug 2016, at 15:31, Martin MOKREJŠ > > wrote: >> >> "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 k

Re: [Samtools-help] samtools calmd behavior and MD tag

> On 2 Aug 2016, at 15:31, Martin MOKREJŠ wrote: > > "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 f

Re: [Samtools-help] samtools calmd behavior and MD tag

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 man

Re: [Samtools-help] samtools calmd behavior and MD tag

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 d

Re: [Samtools-help] samtools calmd behavior and MD tag

Hi Martin, Adding 'calmdnmrecompindetonly=1' will increase performance further as it will only recompute the MD/NM values if the reference section has ambiguity/N within the span of the reads. Regards, Keiran Raine Principal Bioinformatician Cancer Genome Project Wellcome Trust Sanger Institut

Re: [Samtools-help] samtools calmd behavior and MD tag

Heng Li wrote: > samtools calmd does not really work with name sorted files. It spent all the > 12 hours to repeatedly load reference fasta. Hmm, although I did it in the pipeline originally in these steps: samtools sort -@ $xthreads -n -m 4G -O bam -T "$sample" -o "$sample".realignedtogether.B

Re: [Samtools-help] samtools calmd behavior and MD tag

samtools calmd does not really work with name sorted files. It spent all the 12 hours to repeatedly load reference fasta. Heng On Aug 2, 2016, at 9:47 AM, Martin MOKREJŠ wrote: > Keiran Raine wrote: >> For BAM in/out yes: >> >> inputthreads=<[1]>: input helper threads (for inputfo

Re: [Samtools-help] samtools calmd behavior and MD tag

Keiran Raine wrote: > 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) bamsort fixmates=1 calmdnm=1 calmdnmreference="$reference"

Re: [Samtools-help] samtools calmd behavior and MD tag

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 Inst

Re: [Samtools-help] samtools calmd behavior and MD tag

Opened as https://github.com/lh3/bwa/issues/82 , feel free to chim in. -- ___ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/l

Re: [Samtools-help] samtools calmd behavior and MD tag

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

Re: [Samtools-help] samtools calmd behavior and MD tag

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 positio

Re: [Samtools-help] samtools calmd behavior and MD tag

James Bonfield wrote: > On Tue, Aug 02, 2016 at 11:57:52AM +0200, Martin MOKREJ? wrote: >> Could samtools calmd apply the following logic for bwa-processed input? >> Get positions of all N's in the read. >> Do not complain about those positions which are based on N's. >> Do report other position

Re: [Samtools-help] samtools calmd behavior and MD tag

On Tue, Aug 02, 2016 at 11:57:52AM +0200, Martin MOKREJ? wrote: > Could samtools calmd apply the following logic for bwa-processed input? > Get positions of all N's in the read. > Do not complain about those positions which are based on N's. > Do report other positions. I don't entirely underst

Re: [Samtools-help] samtools calmd behavior and MD tag

Hi James, thank you for a detailed analysis. James Bonfield wrote: > On Thu, Jul 28, 2016 at 10:53:53AM +0200, Martin MOKREJ? wrote: >> $ samtools view dedup.realigned.calmd.bam | grep >> HWI-x:xxx:x:1:1106:17285:41358 >> HWI-x:xxx:x:1:1106:17285:41358 145 1