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 ([email protected]) 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. _______________________________________________ Samtools-help mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/samtools-help
