Finding amino acid changing SNPs

To find the amino acid changing SNPs we will use the aaChanges tool in the section Phenotype association (red arrow). Select the results after the controls were removed as the SNP dataset. Looking at the history panel we see that the alleles are in the 5th column (blue box), so select "c5" for the column with the SNPs. For the Gene dataset choose the RefSeq genes we just brought in. We want to keep the columns from our SNP dataset. We only need to know if a SNP causes a change in one gene or transcript. We don't need the same SNP returned for every splice variant where this causes an amino acid change. It will return the first one it finds. The strand information is for the alleles and they are all plus strand. Click the Execute button.

After this tool is done, check the metadata and make sure the columns for the interval format are chosen correctly. Use the pencil icon to make changes.