Question: How to obtain ancestral alleles based on Hg19 genome coordinates?
0
gravatar for devenvyas
5.0 years ago by
devenvyas650
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 ftp://ftp.ensembl.org/pub/release-82/fasta/ancestral_alleles/homo_sapiens.tar.gz, 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:

http://www.1000genomes.org/faq/where-does-ancestral-allele-information-your-variants-come

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
2
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.

http://genome.cshlp.org/content/22/12/2455.long

ADD REPLYlink written 5.0 years ago by Sishuo Wang200
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1843 users visited in the last hour