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!