Mpileup with vcf output? How to change galaxy to older version?

tool-version
tool-search
mpileup
vcf
variant

#1

Hello,

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.


#2

For history download/upload/transfer help, please see this recent Q&A: transfer history from my account on one Galaxy server to another Galaxy server

And this screenshot shows how to search for the Mpileup-related tools available at Galaxy Main (https://usegalaxy.org) and where the versions menu is located (same placement on all tool forms):


#3

Thanks @jennaj!

I was able to switch to 2.1.3 however it was still not usefull due to the maximum read depth that it allows (around a 1000, and I needed aroun 1 million).


Change pileup to vcf format allowing for great depth (100.000 reads)???
#4

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