two allele frequency

Question

[raalsuwaidi]

Hi all,

i am new to bioinformatics so i would really appreciate your help.

i used bcftools to fill the tags for a vcf file and extract the allele frequency. for some positions I get two allele frequencies comma separated. what does it mean?

Answer 1

[Jorge Amigo]

From the VCF format description, the ALT column may contain a "comma separated list of alternate non-reference alleles called on at least one of the samples". This means that all the non-reference alleles that appeared in all samples of the VCF file for a particular variant should be listed in the ALT column and referenced by its index (0 reference, 1 first alternative allele, 2 second alternative allele,...) in each sample's genotype field GT.