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samtools BAQ difference between 0.1.18 and 1.2 version

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  • samtools BAQ difference between 0.1.18 and 1.2 version

    Hi, there
    I compare the mpileup outputs between samtools 1.2 and 0.1.18. And I find
    some discordance of the base quality between the old and new version.
    I extract the pileup file with -B option to disable BAQ of samtools firstly. And I get a position like this:
    gi|57116681|ref|NC_000962.2| 104830 C 23 AAAAAAAAAAAAAAaAAAAAAA^IA BBBB?@@ABBB@=@?C>ABBCB;

    Then I perform the same command except the -B option, but for 0.1.18, I get this:
    gi|57116681|ref|NC_000962.2| 104830 C 23 AAAAAAAAAAAAAAaAAAAAAA^IA <<<<>>:=;<<5=@;:>==;::'
    for 1.2:
    gi|57116681|ref|NC_000962.2| 104830 C 23 AAAAAAAAAAAAAAaAAAAAAA^IA BBBB?@@ABBB@=@?C>ABBCB'

    There is a huge difference of the base quality between these two version. The old version seems change base quality a lot.
    I failed to find such information through google. I am confused about this. Did I miss something?
    Thanks

  • #2
    Different algorithms will give different results; I don't really see what's surprising. Specifically, probability calculations are highly variable because they are subjective; so, it's not unlikely that different versions of a program that does probabilistic calculations will give vastly different results.

    For the record, my company still uses samtools 0.1.19 due to problems with more recent versions.

    Comment


    • #3
      Hi, Brian
      Do you mean different algorithms have been used by these two version?
      The different base quality will influence the downstream SNPs analysis. If I perform base quality filter >20 and strand filter with Varscan2. I will get the SNP at this position from old version but not 1.2 version. Is it normal?

      Thanks!

      Comment

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