Prepare Allele Frequency input file for Sweepfinder2
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7 weeks ago
524730309 • 0

Hi, there. I have some problems about converting vcf to the inputfile of Sweepfinder2. According to the Manual of Sweepfinder2, the forth columns of the input file is the indicator as to whether the site has been polarized (i.e., whether it is known that the allele is derived or ancestral). Since I don't see AA (ancestral allele) in the info-filed of my vcf, there is no way that I can find out which one is ancestral or derived allele?

SNP VCF Sweepfinder2 • 104 views
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