ancestral allele SNP mouse biomart

Question

[serpalma.v]

Dear all

I am trying to get the ancestral alleles for a set of SNPs (10K) using ensembl biomart. Almost all SNPs appear in dbSNP (98%).

When I run a query on biomart to get the ancestral alleles for these SNPs, it returns an empty field for the corresponding attribute ('allele_1').

Here's how I have constructed the query:

ensembl <- useEnsembl(biomart = 'snps', dataset = 'mmusculus_snp', version = '93')

bm_res <- getBM(attributes = c('refsnp_id','chr_name', 'chrom_start', 'chrom_end', 'allele_1'), filters = c('chr_name','start','end'), values = list(chr,start, end), mart = ensembl)

Does this mean that there are no available ancestral alleles for mouse on ensembl?

I appreciate your feedback and thank you!

Answer 1

[Emily]

Ancestral alleles are only available for human genetic variants. I'm not sure why this is an available attribute when there's no data.

Also, for queries of 10k variants, we recommend using the VEP, not BioMart.

[serpalma.v]

thank you for the promp reply.

In a previous related post you recomended to use a standalone script.

The script is quite old and I am not sure if it has been published, do you think it would be a valid alternative to get the ancestral alleles I need?

[Emily]

As far as I'm aware it still works.