I have a list of 100 genes for which (in fact, for one of their transcripts in particular) I would like to get "synonymous coding" and "non-synonymous coding" SNPs that are observed in 1000G data (n=629).
Moreover, it would be fantastic to somehow extract the heterozygosity status for those SNPs.
I tried the ENSEMBLE 1000G browser, however, there are inconsistencies, that is, some SNPs that appear in the VCF file do not show up in the browser view. In addition, I do not want to mess with the dbSNP but am only interested in the SNPs observed in 1000G.
Any help would be much appreciated.