Re: [Samtools-help] inconsistency in samtools mpilup basequality [EXT]

[James B. <jk...@sa...>]

On Fri, Jun 14, 2019 at 02:33:50PM +0000, Karina Borlaug wrote:
> Hi I am seeing some inconsistency in the samtools mpilup. It seems to report a mix of phred + 33 and phred + 64  for the basequality in a .bam file. However when viewing the same .bam file using samtools view it appears to only use phred +33.
> 
> I am using  samtools/1.8
> 
> Eksample:
> 
> $samtools mpileup -r 1:43149119-43149119 -q 0 -Q 0 -f Hg19.fasta sample.bam

The +64 is simply a modified base quality coming in via the BAQ
calculation.

If you add the "-B" option you'll probably see the qualities you
expect, however this may not be what you want.  See
https://academic.oup.com/bioinformatics/article/27/8/1157/227268 for
more information on what BAQ is doing.

James

-- 
James Bonfield (jk...@sa...)
The Sanger Institute, Hinxton, Cambs, CB10 1SA


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