Hello all,
I've downloaded a subset of SNPs using tabix and then did an allele count using vcftools. I used the -get-INFO AA to get the identity of the ancestral allele for my SNPs but it returned all question marks.
My question is, what is the next best way to get ancestral alleles from the 1000 genomes SNPs dataset. I've tried using UCSCs liftover to chimp and macaque, but the alleles don't always match up (i.e. sometimes the ancestral allele is neither one of the human variants).
Any help would be greatly appreciated.
I've downloaded a subset of SNPs using tabix and then did an allele count using vcftools. I used the -get-INFO AA to get the identity of the ancestral allele for my SNPs but it returned all question marks.
My question is, what is the next best way to get ancestral alleles from the 1000 genomes SNPs dataset. I've tried using UCSCs liftover to chimp and macaque, but the alleles don't always match up (i.e. sometimes the ancestral allele is neither one of the human variants).
Any help would be greatly appreciated.
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