Assign SNPs on chromosome 0

apriha / snps

tools for reading, writing, merging, and remapping SNPs

BSD 3-Clause "New" or "Revised" License

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Assign SNPs on chromosome 0 #13

Open apriha opened 5 years ago

apriha commented 5 years ago

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.

willgdjones commented 4 years ago

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.

apriha commented 4 years ago

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.