Discussion

This example was tuned to find the known SNP. There are some places where the filtering can be adjusted to find similar SNPs that are not exactly like this one. If you find that you are not getting any or very few results you can adjust the definition of "mostly fixed" to 80 or 85%. In the clustering step you can require fewer SNPs or allow a larger spacing. Using different SNP sets has an effect as well. Generally the more individuals you use the fewer SNPs that will meet the criteria. This can be helpful if you are getting too many SNPs for further testing. Another option for too many SNPs is to do the opposite of the previous suggestions and tighten the criteria. However, there is a danger in getting the count too low that you are discarding the SNP you are looking for. Galaxy fortunately makes it simple to rerun the queries trying different criteria.