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Greetings all.
Can someone here point me towards a good source of information on the Extended BAQ algorithm implemented in mpileup in SAMtools?
This algorithm modifies the Base Alignment Qualities (BAQ) correction for variants, which minimizes false positives near indels. There is ample information out there on BAQ, however, for the Extended BAQ (-E option in making mpileup files), I can find nothing. I even wrote Heng Li an email directly about it, but no response.
I find using the Extended BAQ to be the best possible way to call SNPs, as it maximized true positives over false negatives (problem with BAQ) and false positives (problem with using no correction at all). However, I don't feel I can just keep using this blindly without knowing how it works.
Any help is most appreciated.
Can someone here point me towards a good source of information on the Extended BAQ algorithm implemented in mpileup in SAMtools?
This algorithm modifies the Base Alignment Qualities (BAQ) correction for variants, which minimizes false positives near indels. There is ample information out there on BAQ, however, for the Extended BAQ (-E option in making mpileup files), I can find nothing. I even wrote Heng Li an email directly about it, but no response.
I find using the Extended BAQ to be the best possible way to call SNPs, as it maximized true positives over false negatives (problem with BAQ) and false positives (problem with using no correction at all). However, I don't feel I can just keep using this blindly without knowing how it works.
Any help is most appreciated.