Reference File Creation for Camelids

[conor-ohare]

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!

[BenjaminPeter]

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.

[conor-ohare]

Great, thank you for the response and for providing those links :)