Thank you that solved it! ________________________________ Fra: Robert Davies <r...@sanger.ac.uk> Sendt: mandag 17. juni 2019 15:34 Til: Karina Borlaug Kopi: samtools-help@lists.sourceforge.net Emne: Re: [Samtools-help] inconsistency in samtools mpilup basequality [EXT]
On Mon, 17 Jun 2019, Karina Borlaug wrote: > I tried this command instead: > > $samtools mpileup -r 1:43149119-43149119 -q 0 -Q 0 -B -f Hg19.fasta sample.bam > > But got the exact same output as without the -B option. > > However as you point out it might be more valuable to keep the BAQ. > > I am trying to extract the quality values with a python script in order to > create a frequency plot . I am still a little confused on why they are mixed > +33 and +64. Does it mean all of the ascii character in the output string is > BAQ scores and only some of them was converted to +64? > > output string : > b>^=_=@=??]@A^AAbBBccBAcBBcB<LcBBBcBAA>BcBAABcBBcAb,AcCBC,CBBCddCBBBdCCCBcBBBACCBBC?cdBC!8A!c!C!CBBCBB?CC7CABA!aaAB@B!Bc!CCBC;CCABC!cCBAB!CB!BBd@B!?CB@ABC!A!CC!B`Bb!C!!!!!CCA?B<CC!BBCCCCCCCAC!CCAACA!A!!!!!!A!=!=A! > > Or does it mean that only the +64 values are BAQ scores and the remaining > +33 character are normal basequality values resulting in having to separate > the two different values when plotting a frequency plot. I doubt that BAQ is the cause, as it should only reduce quality values and never increase them. You might instead be seeing the result of the overlap detection. This changes the quality values in read pairs where the forward and reverse reads are long enough to overlap each other. Where that happens, the lower-quality base in the pair will be set to zero and the higher-quailty one to the sum of the two original quality values if they agree, or to 0.8 x the highest if they disagree. To turn this off, try the `-x` option: samtools mpileup -r 1:43149119-43149119 -q 0 -Q 0 -B -x -f Hg19.fasta sample.bam Rob Davies r...@sanger.ac.uk The Sanger Institute http://www.sanger.ac.uk/ Hinxton, Cambs., Tel. +44 (1223) 834244 CB10 1SA, U.K. Fax. +44 (1223) 494919 -- 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.
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