Disambiguation between allelic fraction and allele frequency

[chabriera]

Could you please find alternate name shortenings for allelic fraction and allele frequency instead of AF for both?
Thanks :)

[tdelhomme]

What about MAF (minor allele frequency) instead of allele frequency?

[mfoll]

MAF is a good idea only if we report the minor allele frequency:

the frequency at which the second most common allele occurs in a given population

[mfoll]

I like VAF for the allelic fraction

[mfoll]

AAF for "alternate allele frequency"?

[tdelhomme]

Yes I like also VAF for individual allelic fraction.

[mfoll]

VCF specification has a reserved INFO/AF field:

AF : allele frequency for each ALT allele in the same order as listed: use this when estimated from primary data, not called genotypes

But we estimate it from called genotypes, so AF is not good.

[mfoll]

Actually what we call INFO/AF at the moment is not the allele frequency but the frequency of samples being 0/1 or 1/1: https://github.com/IARCbioinfo/needlestack/blob/v1.1b/bin/needlestack.r#L397

[tdelhomme]

VF for variant frequency?

[tdelhomme]

Does GATK not respect the VCF specification? https://gatkforums.broadinstitute.org/gatk/discussion/6202/vcf-file-and-allele-frequency