Can Truffle work on a small number of individuals?

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PeggyTuber
Guest

Can Truffle work on a small number of individuals? Jun 12, 2020 4:56:12 GMT

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Post by PeggyTuber on Jun 12, 2020 4:56:12 GMT

Hi,

I am new to IBD analysis and it's great to find Truffle. May I know if Truffle works on only 6-10 individuals to calculate IBD?
The species I am working on is tetraploid and my sequence data are unphased (3-4 haplotypes on each locus).
Does Truffle suitable for this kind of data?

Thanks,

Best,
Peggy

Apostolos Dimitromanolakis
Administrator

Posts: 3

Can Truffle work on a small number of individuals? Jul 11, 2020 10:56:58 GMT

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Post by Apostolos Dimitromanolakis on Jul 11, 2020 10:56:58 GMT

Hi, it should be no problem working with a small number of individuals. We have not tested truffle with tetraploid data, how is your vcf file formatted? Truffle was degisned to work with 2 genotypes per locus, i.e. 0/1, 0/0, or 1/1. Assuming you can transform your data to this format then it should be no problem.

Can Truffle work on a small number of individuals?

Post by PeggyTuber on Jun 12, 2020 4:56:12 GMT

Post by Apostolos Dimitromanolakis on Jul 11, 2020 10:56:58 GMT

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