Question: VCFTools weir-fst-pop on haploid organisms
0
gravatar for kawaiilain
4.9 years ago by
kawaiilain10
United States
kawaiilain10 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 • 2.2k views
ADD COMMENTlink modified 24 months ago by guillaume.rbt530 • written 4.9 years ago by kawaiilain10

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

ADD REPLYlink written 24 months ago by guillaume.rbt530
1
gravatar for Adrian Pelin
4.9 years ago by
Adrian Pelin2.2k
Canada
Adrian Pelin2.2k wrote:

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

ADD COMMENTlink written 4.9 years ago by Adrian Pelin2.2k
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 4.9 years ago by kawaiilain10
0
gravatar for guillaume.rbt
24 months ago by
guillaume.rbt530
France
guillaume.rbt530 wrote:

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

ADD COMMENTlink modified 24 months ago • written 24 months ago by guillaume.rbt530
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