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Disambiguation between allelic fraction and allele frequency #181
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What about MAF (minor allele frequency) instead of allele frequency? |
MAF is a good idea only if we report the minor allele frequency:
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I like VAF for the allelic fraction |
AAF for "alternate allele frequency"? |
Yes I like also VAF for individual allelic fraction. |
VCF specification has a reserved INFO/AF field:
But we estimate it from called genotypes, so AF is not good. |
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 |
VF for variant frequency? |
Does GATK not respect the VCF specification? https://gatkforums.broadinstitute.org/gatk/discussion/6202/vcf-file-and-allele-frequency |
Could you please find alternate name shortenings for allelic fraction and allele frequency instead of AF for both?
Thanks :)
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