Bayesian Inference in SAMtools/BCFtools

[elfuser]

Hello:
I am using BWA + SAMtools/BCFtools to reference map assemble illumina reads and call SNPs in a bacterial genome respectively. I use the command:

bcftools view -bvcg input.bcf > output.bcf

which is supposed to filter the initial pileup and call the variant positions using bayesian inference similar to the one used in MAQ.

I'm not an expert in statistics, but I would like to know what are the priors and posteriors calculated. Thanks very much!

[Heisman]

You might be interested in this paper: http://www.cbcb.umd.edu/~hcorrada/CM...gs/Li_2011.pdf

[elfuser]

@Heisman I thinks this is what I was looking for, thanks