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Old 05-07-2013, 11:50 AM   #1
Location: Georgia

Join Date: Mar 2013
Posts: 15
Default how to compute Minor Allele Frequency for a variant call?

I am interested in computing the minor allele frequency (MAF) for each variant or SNP call in the RNA-seq data obtained from Varscan calling method. Is it as simple as the fraction of number of variant alleles divided by the total number of alleles across all samples for each variant? For example, I have four samples with 4 genotypes for a SNP call

S1 = GG
S2 = GC
S3 = GC
S4 = GG

I computed the variant allele frequency (C) as 2/8 i.e. 0.25. Is this the MAF? I am interested in SNPs < 1% minor allele frequency that are rare, unknown and potentially clinically associated. But I don't think my data set can have MAF of 1% from the way I am computing it. Any suggestions?

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