Question: How to obtain ancestral alleles based on Hg19 genome coordinates?
gravatar for devenvyas
5.0 years ago by
Stony Brook
devenvyas650 wrote:

I'm trying to obtain ancestral alleles for almost 600,000 (i.e., Human-Chimp common ancestor) SNPs. A lot of them have dbSNP rs #s, but a lot of them don't.

I am particularly lost in how to obtain these data and am wondering if someone can point me in the right direction.


snp • 3.1k views
ADD COMMENTlink modified 5.0 years ago • written 5.0 years ago by devenvyas650

But how would I extract that data from the 1000 Genomes project?

That thread confused me a bit, so they are saying the ancestral alleles from 1000genomes are representative of the human-chimp common ancestor from Ensembl?

Also, I stumbled across, but I was unclear whether this is equivalent to the Human-Chimp ancestor. I was wondering if someone could help on this matter. Thanks!

ADD REPLYlink modified 11 months ago by RamRS30k • written 5.0 years ago by devenvyas650

historically, primates' alleles were used as ancestral alleles for evolutionary reasons. dbSNP used the chimp's, and Ensembl used the macaque's when I first started working with these huge resources, a few years ago. right now, 1000g uses a combination of primates which allows them to provide a deeper (and, in my opinion, a more appropriate) ancestral description:

by the way, the link you provide is a fasta file. if you would like to get a particular base from there I would suggest using samtools faidx, although querying 1000g variants directly may be all you may need.

ADD REPLYlink modified 5.0 years ago • written 5.0 years ago by Jorge Amigo12k
gravatar for Sishuo Wang
5.0 years ago by
Sishuo Wang200
The Chinese University of Hong Kong
Sishuo Wang200 wrote:

The following link might be helpful I think.

1000 Genomes Snps' Ancestral Allele

ADD COMMENTlink written 5.0 years ago by Sishuo Wang200

Also, the following paper uses a ML method to infer ancestral alleles which might be more complicated than the way mentioned in the link above.

ADD REPLYlink written 5.0 years ago by Sishuo Wang200
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