I am using ADTEx to perform copy number analysis of some exome sequencing data. ADTEx requires a B-allele frequency file in order to perform ploidy estimation and genotype prediction. However, I do not know how to create such file and the ADTEx tutorial does not explain it either. I was wondering if there is a general way to create B-allele frequency files that I do not know of!
The file as is explained in the tutorial should have the following fields:
chrom- chromosome name (same format as in BED or BAM file)
SNP_loc- location of the SNP
control_BAF- B allele frequency (BAF) at each SNP in control sample
tumor_BAF- B allele frequency (BAF) at each SNP in tumor sample
control_doc- Total read count at each SNP in control sample
tumor_doc- Total read count at each SNP in tumour sample
I would like to thank you in advance for your responses and wishing you all a nice summer.