Hi,

Do anyone know how to calculate BAF(B-allele frequency) and log R ratio from SNP calling pipeline( bcftoools mpileup & call) ?

I read some papers and I guess BAF can be calculated by (AD[2]/DP) and LRR can be calculated by [log2(cancer DP /normal DP)] , are that right?

I also want to know the level of allele specific CNV using ASCAT package. now I have paired samples (normal WGS and cancer WGS data), ASCAT need BAF and LRR from tumour and gemerline, but how to differ the tumour and gemerline variation?

Hi @xiaoguang! Did you figure out if this is a valid way to calculate BAF and LRR?