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Old 07-27-2010, 01:51 PM   #1
Location: canada

Join Date: May 2010
Posts: 16
Default Samtools pileup indel quality score computation

Sorry if this question has been asked before (if yes, please direct me to the appropriate link); I also checked the MAQ paper but could not find an answer to this question:
How does samtools pileup command compute the snp and indel quality score.
I am simply looking for the basic idea rather than the gory formula.
Surely, it is some function of the mapping quality and the basequality.
However, I have been unable to decipher the meaning of BWA's mapping quality (except that when it is 0 it means there is multiple regions to which a read maps to equally well). I understand what the score represents in the probability sense; I simple don't know how it is computed.

The reason I ask is that I am working on calling a snp caller using simple heuristics and I start with readBases and the quality scores of read bases at a given site. However, I would like to compute the snp, indel quality.
One straight forward approach is that I simply take the mean of the basequality at the variant position. What is wrong with this?
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