Quality based callers such as the ones implemented in MAQ, CLC Bio, and Atlas use NQS (Neighborhood Quality Standard) score. But unfortunately, I am not aware that any of these tools provides a straight forward way to compute NQS scores directly from a bam file or pileup. There are tons of published papers that utilized NQS, and I am just wondering if there is any easy way to calculate NQS from Bam?

Thanks.