converting vcf to genepop with pgdspider for lositan

Question

[jf]

Hello, I am using the output vcf from tassel uneak as the input vcf for pgdspider. Then I am trying to use pgd spider to convert the file to genepop for lositan to find outlier snps. In pgd spider I am inputting a population definitions file like:

Fe-36 TW_1 Fe-51 TW_1 Fe-76 TW_1

there are 4 populations: TW_1, 2, 3, ad 4. But when I load the file into lositan, it is only recognizing one population.

are there any oversights on my part that could result in that conversion error?

Answer 1

[g3.prashanna]

Hi,

Maybe it is too late to answer.

Add the pop between the groups of the population. for eg.

pop fe36-1 fe36-2 fe36-3 pop Tw_1 Tw_1_a Tw_1_b pop Fe-51_1 Fe_51-2

This will separate three populations i.e. Fe-36, Tw_1 and Fe-51.

You can also edit the population names in lositan afterwards.

Thanks