VCFTools weir-fst-pop on haploid organisms
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7.6 years ago
kawaiilain ▴ 30

Hello,

Is it possible to use vcftools weir-fst-pop on haploid genomes? I do not seem to be able to find any option to specify the ploidy of my samples.

Thank you in advance.

vcftools weir-fst-pop haploid fst • 3.3k views
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Hi, Have you actually found a solution? (I have the question)

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7.6 years ago
Adrian Pelin ★ 2.5k

Fst involves measuring expected heterozygosity. Given that, it is impossible to calculate Fst for haploid organisms.

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Technically you can calculate Fst for haploids using haplotype diversity instead of heterozigosity, but I guess vcftools does not take that into consideration. Thank you for your reply.

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4.7 years ago
guillaume.rbt ▴ 930

update : Does anyone would know a tool that computes FST on haploid populations thanks to SNPs data? Thanks

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