Samtools Vcf Reference And Alternate Alleles

Question

[FGV]

I'm having some trouble dealing with samtools VCF files. These files have a field for the reference and another for the alternate allele, but shouldn't this be instead major/minor alleles??

I mean, in the example below, position 335 on chr01 has a G and T with freqT=0.2607. chromosome01 335 . G T 19.3 . DP=7;AF1=0.2607;AC1=2;....

How would VCF depict a case of a position where the reference was "G" (like above) but where freqT=0.3 and freqA=0.7?? that is, where none of the alleles is equal to the reference.

thanks FGV

Answer 1

[swbarnes2]

vcfs can put two different alleles in the ALT column, separated by commas. That's what it would do.

[FGV]

but then, how would the allele frequencies be displayed for each ALT? two AF1 fields?

[Laura]

most people use a comma delimited string in the same order as the alt field