Hi,
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?
thanks
Lee
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?
thanks
Lee