Open conor-ohare opened 1 year ago
Hi Conor,
I think that looks right (minus indentation and formatting).
Maybe it helps to look at the examples in the tests, where I use this command using this pops.yaml file using this vcf-file.
Great, thank you for the response and for providing those links :)
I want to create a reference file to determine the ancestry of ancient camelid samples I have. I want to consider two ancestral populations: the guanaco and the vicuña. My approach is the following:
1) Create a .vcf using the command
./angsd -b list.list -dovcf 1 -gl 1 -dopost 1 -domajorminor 1 -domaf 1 -snp_pval 1e-6
where list.list are my samples (3 from guanaco, 3 from vicuña, and 1 camel to act as an outgroup).
2) Use this .vcf in the command:
admixfrog-ref --vcf [output] --out x.ref.xz \ --states GUA VIC \ --pop-file data.yaml
where the .yaml file looks like:`GUA -GUA_Sample1 -GUA_Sample2 -GUA_Sample3 VIC -VIC_Sample1 -VIC_Sample2 -VIC_Sample3
pseudo-haploid -Camel `
which will output the reference file.
Have I understood this correctly? What I am confused by is that the STATES in the provided code in the documentation do not match those in the .yaml file.
Any help would be greatly appreciated!