How is allelle frequency calculated ?

This a variation where Allelle Frequency (AF) is 0.500 and AD = 57,36 and DP = 93

My understanding about AF calculation is 36 / 93 = 0.387096774

chr1    976215  rs7417106   A   G   687.60  .   AC=1;AF=0.500;AN=2;BaseQRankSum=0.978;DB;DP=93;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=7.39;ReadPosRankSum=1.018;SOR=0.666    GT:AD:DP:GQ:PL  0/1:57,36:93:99:695,0,1225

vcf allelle frequency exome

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updated 5.5 years ago by Pierre Lindenbaum

• written 5.5 years ago by DareDevil

1 answer

One diploid genotype.

total number of alleles AN= n-genotypes * ploidy = 2

total number of ALT alleles AC= samples is HET (0/1) = 1

alllele frequency AF= AC/AN = 1/2 = 0.5

AD and DP are unrelated to AF.

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written 5.5 years ago by Pierre Lindenbaum

@Pierre Lindenbaum Thanks for the quick reply!!.

But if you look at this post, they mention about AD and DP for calculating AF

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written 5.5 years ago by DareDevil

they mention about AD and DP for calculating AF.

and what is the conclusion of the post you mentioned ?

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written 5.5 years ago by Pierre Lindenbaum

there is no precised conclusion there. But if you look at these following post here and here. They mention about relating AD and DP in calculating varint allelle frequncy

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written 5.5 years ago by DareDevil

add VAF or FREQ in vcf file from read depth and Calculation of VAF (variant allele frequency) are about VARIANT allele frequency NOT **allele frequency'

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written 5.5 years ago by Pierre Lindenbaum

Thanks.. Little confused with the terms

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written 5.5 years ago by DareDevil

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