Adding the reference allele

The conversion tool for creating gd_snp tables needs to know the reference allele, so we will add it to our pgSnp files before converting them to gd_snp format. In the Fetch Sequences section there is a tool called Extract Genomic DNA. Run this tool on the CEU dataset, using the settings indicated below (red arrows). When the source is "locally cached", Galaxy uses the "database" information from the metadata (blue arrow) to know which sequence to use. Click the Execute button (green arrow).

Now repeat this step adding the reference to each of the SNP files. Rename the datasets to make the history easier to follow.