Heterolasmy and VCF files
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17 months ago
paolo ▴ 70

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?

heteroplasmy VCF • 875 views
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Entering edit mode
17 months ago

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)

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Thanks for the tip!

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