Batch query of ancestral and derived alleles from Ensembl

Question

[Mr Locuace]

Hello,

I would like to know whether there is a way of getting ancestral and derived alleles for a batch of thousands of SNPs on the Ensemble web page. I know this can be done in the dbNCBI Database. The problem is that NCBI ancestral data was updated on 2004!

dbSNP ancestral allele data was submitted by Dr. Jim Mullikin of the National Human Genome Research Institute (NHGRI). Dr. Mullikin derived his ancestral allele data by by the comparison of human DNA to chimpanzee DNA, and his methodology is available online at PLoS. The last time Dr. Mullikin provided us with ancestral data was in May 2004.

Thanks very much

Answer 1

[linnaean]

You could derive the ancestral alleles from the Ensembl vcfs. For instance, you could download the vcf from Ensembl 92 (which is from 2018) at: ftp://ftp.ensembl.org/pub/release-92/variation/vcf/homo_sapiens/homo_sapiens.vcf.gz

The VCF includes ancestral alleles so you could find your SNPs of interest and extract their ancestral alleles.