I have gotten SNP data on a number of regions via UCSC genome browser. I have assigned all SNPs within a region to a unique identifier (eg 001, 002 etc) using a dataset of my own and using the join on genomic intervals tool. However, I now wish to know how many SNPs belong to each unique identifier. How might I go about doing this?
If you want to count the number of variants in genes then SNPeff. gives such a report for genes. This will be possible on usegalaxy.org if you are working with a reference genomes which is already present as a drop down option.
What you want to do seams easy but I cannot think of another way off the top of my head. say if you found another way. Cheers