Gabriel Renaud
Gabriel Renaud
Can you please post a few of the lines that are causing the problem?
Yes, normally you get 3 values for PL, homo ref, het, homo alt. How did you get "0,45" for example?
is this haploid data?
I see! Normally I would modify the code to handle this but can you either code it yourself or ask chatgpt/claude to transform the GT from 0 = 0/0 1...
Dear Mohammed, a quick question before, isn't BetaScan configured for balancing selection and considers heterozygous advantage?
sure but I would question what do the results even mean for haploid data. I would suggest asking Katie Siewert-Rocks directly.
That is very tough! What is much easier is to transform that VCF to ACF, and use the specific population as the root/anc. However be wary that you don't really...
Yes! You need to convert VCF to ACF and run replaceancestor I believe. Let me know if that works!
> Thank you. I will try it ! If I use vcfm2acf to convert VCF to ACF , then I use usepopsrootanc to tell the root(outgroup), finally I use the...
> Hello, I have another question. Is the file2.acf.gz in https://github.com/grenaud/glactools the result using the glactools with vcfm2acf --onlyGT --fai parameter? I am not sure if using these parameters is...