Heterolasmy and VCF files

Question

[paolo]

Can heteroplasmy of mitochondrial calls be deduced from one of the subfields of the VCF file? For instance, can I simply say that AF of the FORMAT column is equal to heteroplasmy?

Answer 1

[Jeremy Leipzig]

i would rely on the AD (allelic depth) of each sample in reads. By the time the reads are aggregated into the AF i wouldn't trust variant callers not to corrupt those numbers as they are expecting a biallelic genome. (GATK has become better at this)

[paolo]

Thanks for the tip!