How is allelle frequency calculated ?
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2.4 years ago
dare_devil ★ 3.1k

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 • 737 views
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2.4 years ago

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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@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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and what is the conclusion of the post you mentioned ?

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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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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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Thanks.. Little confused with the terms