how to calculate BAF and LRR from VCF or BCF files?
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8 weeks ago
xiaoguang ▴ 90

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?

SNP BAF LRR Variation • 178 views
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