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!
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