The “mpileup” tool that gives an output file in vcf format is not available in usegallaxy.org. However I read a post on biostar (https://biostar.usegalaxy.org/p/29664/) stating that previous versions had it and that usegalaxy.org.au has it still now. I tried to follow the instructions to be able to set up the older version in order to be able to use it in usegalaxy.org, but I was unable to find the “tool form” and the “Versions” menu to switch to version
2.1.3 of the tool. Would you please elaborate more, including maybe print screen photos, so I can actually go on with the version switching?
There was also the suggestion to use VarScan instead but that option does not allow me to set a minimum quality score per base, and I was unable to find the “behind the scenes” settings this algorithm uses to check if the default settings suit my needs.
I also tried to share my history from usegalaxy.org to usegalaxy.org.au and kept on getting errors. Is it possible to share the history between 2 different galaxy servers? If so, how?
I appreciate any help on this. I am new to NGS data, and I find commands very difficult, so given that Galaxy is very user friendly, I can only continue my analyses using it.