Entering edit mode
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
@Pierre Lindenbaum Thanks for the quick reply!!.
But if you look at this post, they mention about
and what is the conclusion of the post you mentioned ?
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
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'
Thanks.. Little confused with the terms