get the list of ancestry sites?

[PhillipMaire]

Hey can you help me find a reference list of the sites you compare against? or the sites identified by somalier. for example when i run the docker container i get the message of
[somalier] found 2937 sites
and I just want to be able to pull these from my VCF file and do some custom analysis

[brentp]

Hi, that's not really possible. I guess you could recreate the simple filters used in somalier and then iterate over the sites file.

[PhillipMaire]

Ok, thanks for the reply. I am new to genetics and am finding it difficult to get lists of probes that are related to certain categories (e.g., ancestry, cancer, etc.). So you are saying even if I forked your repo, edited the code, and recompiled it, there is nowhere in your codebase where these probe names/numbers or some IDs could be extracted? I was assuming that there was a comparison somewhere, and at each site, upon a "match" (or filter pass), there would be some ID I would have access to that I could save as a text file somewhere.

I could edit the code and rebuild the Docker image, but I just wanted you to point me to which piece of code would have that info. If my thinking is wrong on this, then no worries, but I thought this shouldn’t be too hard in theory since I would assume the probes that pass the filter must be somewhere in the code.

[brentp]

ah, ok. so if you're willing to do that, you can look here:
https://github.com/brentp/somalier/blob/master/src/somalier.nim#L109-L159

if you get to line 158, the variant passed filters and you can write/save v or site
let me know if any other questions, might be other details i can point you to.

[brentp]

note that these sites won't be the usual "ancestry-informative" sites. they are just sites likely to be assayed in exome (and genome) that are relatively common in the population.

[PhillipMaire]

ok thanks! Both comments are really helpful. I think I can dig into if I need to, but might find another way to get the the list of site.

I am using the illumina Infinium Global Screening Array-24 v3.0 BeadChip and they provide all these categories of different markers like "Ancestry-informative markers" and "Somatic mutations in cancer" but nowhere can I find the relevant lists/data of these haha seems so strange to me. I would have thought it to be standard practice to provide data on this but like I said this is all new to me. if you have any thought on this I would appreciate it but no worries considering that is off topic here.

thanks for all your help :)

[brentp]

for ancestry, maybe this: https://pmc.ncbi.nlm.nih.gov/articles/PMC3073397/#SD1

and for somatic mutations, check cosmic.

[PhillipMaire]

wow super kind of you, thanks Brent! have a nice data :)