Question

Any tool to calculate Fst on haploid data?

1

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rkdonthu ▴ 10

@rkdonthu-12441

Last seen 7.8 years ago

Hello,

I could not find any tool/script that calculates FST on haploid data. All the tools that I know of calculate FST on diploid data only. I really appreciate anyone's help in finding a tool for this purpose.

Thank you,

Ravi

snps VCF • 3.0k views

ADD COMMENT • link updated 2.6 years ago by Arafat • 0 • written 7.8 years ago by rkdonthu ▴ 10

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Hi Ravi,

I have the same problem as you.

I know that the R package hierfstat should do this calculation, but I haven't tested it yet.

What kind of data have you ? Have you found a solution?

Thanks,

Guillaume

ADD REPLY • link 7.6 years ago guillaume.rbt • 0

score 0 · Answer 1 · 2022-05-09

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Arafat • 0

@db4cf16b

Last seen 2.6 years ago

United States

You can use genet.dist function from hierfstat library to calculate different Fst estimates from haploid data. Make sure to set diploid=F. A detailed tutorial can be found here: https://arftrhmn.net/fst-for-haploid-data-in-r/

ADD COMMENT • link 2.6 years ago Arafat • 0