Consensus Quality And Snp Quality In Samtools

Question

[Anjan]

From the SAMtools online manual: "Note that consensus quality is the Phred-scaled probability that the consensus is wrong. SNP quality is the Phred-scaled probability that the consensus is identical to the reference. They are different in concept. For SNP calling, SNP quality is of more importance."

How are the probabilities that the consensus call or the SNP call is wrong calculated? The SAM tools papers do not elaborate on this. Will appreciate any pointers. Thanks, Anjan

Answer 1

[Raygozak]

You can look into the statistics of variant calling, specifically from freebayes (another software for variant calling) you can look at their methodology, i don't think it is that different from what samtools uses:

http://arxiv.org/abs/1207.3907