Question: VCFTools weir-fst-pop on haploid organisms
1
gravatar for kawaiilain
5.3 years ago by
kawaiilain20
United States
kawaiilain20 wrote:

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.

fst vcftools haploid weir-fst-pop • 2.3k views
ADD COMMENTlink modified 2.4 years ago by guillaume.rbt620 • written 5.3 years ago by kawaiilain20

Hi, Have you actually found a solution? (I have the question)

ADD REPLYlink written 2.4 years ago by guillaume.rbt620
1
gravatar for Adrian Pelin
5.3 years ago by
Adrian Pelin2.3k
Canada
Adrian Pelin2.3k wrote:

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

ADD COMMENTlink written 5.3 years ago by Adrian Pelin2.3k
1

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.

ADD REPLYlink written 5.3 years ago by kawaiilain20
1
gravatar for guillaume.rbt
2.4 years ago by
guillaume.rbt620
France
guillaume.rbt620 wrote:

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

ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by guillaume.rbt620
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