6 weeks ago by
Yes, MPileup multi-way pileup of variants (Galaxy Version
2.1.4) no longer has this functionality.
But the earlier version of the tool does and is still available at Galaxy Main https://usegalaxy.org, Galaxy EU https://usegalaxy.eu and Galaxy Australia https://usegalaxy.org.au. Open the tool form and use the "Versions" menu at the top to switch to version
2.1.3 of the tool (likely the version you were using before).
You also might want to look at the tools MiModD Variant Calling and VarScan. Both produce VCF results (the first from BAM alignments the same as the older Mpileup did, the other from pileup results).
I asked the developers if there was a specific reason why the full bcftools/vcftools suites are not on the usegalaxy.org/eu public servers at Gitter. The tool bcftools mpileup is available at https://usegalaxy.org.au. Let's see what they reply with and make any new tool install requests based on that feedback. https://gitter.im/galaxyproject/Lobby?at=5bbfa0b6c08b8b3067008a59
Thanks and hope that gives you some options for now, Jen, Galaxy team