Thank you for your answer!
I followed the tutorial you suggested and also the “Identification of somatic and germline variants from tumor and normal sample pairs” tutorial (https://galaxyproject.github.io/training-material/topics/variant-analysis/tutorials/somatic-variants/tutorial.html#variant-annotation-and-reporting), successfully.
1)I am interested in learning more about the GEMINI annotate and query and Join files to customize my analysis. I am trying to download the gnomad database but I am failing in downloading the dataset. It cannot recognize the vcf.bgz.tbi extension, I think.
Would you suggest how can I download this dataset?
2)during the tutorials I realized that the some commands are on usegalaxy.org and others on galaxy Europe. Is there any way to share the history between the two websites?
- Lastly for annotate query, learning SQL language is always needed? Or I can use other command like filter and sort? (to remove frequent variant for example)
Thanks in advance for your help.