Yes, there are several choices.
- One is to perform variant calling on your own data (many are wrapped for Galaxy), then summarize/count by gene or transcript
- Another is to use public SNP data resources and do the same
These tutorials include variant calling and other operations https://github.com/nekrut/galaxy/wiki. The Galaxy 101 (both parts) is a good place to start as it covers many relevant data manipulations.
Take care, Jen, Galaxy team