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Published 20 hours ago • verified publisher icon apriha

Assign SNPs on chromosome 0

Open apriha opened this issue 5 years ago • 2 comments

Some newer Family Tree DNA famfinder files seem to have SNPs assigned to chromosome 0. Similar to SNPs._assign_par_snps, use the RefSNP API to assign each of these SNPs to a chromosome and update the SNP's position to be consistent with the assembly.

apriha avatar Jun 14 '19 06:06 apriha

I have noticed that for AncestryDNA files, the _assign_par_snps step can take a substantial amount of time (> 1 minute), because of repeated API requests. I have currently bypassed this issue by setting assign_par_snps=False. Is there a way we can speed this up with the VCF_endpoint like you suggest in #19.

willgdjones avatar Dec 01 '19 11:12 willgdjones

Yeah, I agree that having a resource like discussed in #19 to lookup SNPs would help here as well and would reduce repeated API calls. I'll start looking into this as part of #42.

apriha avatar Dec 01 '19 16:12 apriha