how to calculate BAF and LRR from VCF or BCF files?
0
0
Entering edit mode
11 months ago
xiaoguang ▴ 120

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 • 679 views
ADD COMMENT
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 2084 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6