Calculating weir-fst by vcftools
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15 days ago
Liangfa • 0

Hi, I'm using vcftools to calculate weir-fst, and getting confused by the result. One of the records is below, two populations, subpop1 and subpop2. I'm using a single SNP (Chr10:28041905) for an example. There are two alleles for this position, A and G. The allele frequency has also been calculated by vcftools. I got the WEIR_AND_COCKERHAM_FST of 0.63175 by vcftools. However, when i tried to calculated Fst by Fst = 1- Hs/Ht, it not equals the result of vcftools. And explanation will be appreciated.

POP CHROM POS N_ALLELES N_CHR {ALLELE:FREQ} {ALLELE:FREQ} Subpop1 Chr10 28041905 2 220 A:0.936364 G:0.0636364 Subpop2 Chr10 28041905 2 6686 A:0.200718 G:0.799282

CHROM POS WEIR_AND_COCKERHAM_FST
Chr10 28041905 0.63175

vcftools • 76 views
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