Question: Mpileup with vcf output?
gravatar for marcelina.parra
6 weeks ago by
marcelina.parra0 wrote:


I noticed that the "mpileup" tool that gives an output file in vcf format is no longer available. I was using it to analyze data on my mutants, then using bcftools call to find the variants. I see that there is samtools mpileup now, but since the output isn't vcf I'm not able to use bcftools call. Would it be possible to install bcftools ( and vcftools ( to Galaxy?

ADD COMMENTlink modified 6 weeks ago by Jennifer Hillman Jackson25k • written 6 weeks ago by marcelina.parra0
gravatar for Jennifer Hillman Jackson
6 weeks ago by
United States
Jennifer Hillman Jackson25k wrote:


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, Galaxy EU and Galaxy Australia 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 public servers at Gitter. The tool bcftools mpileup is available at Let's see what they reply with and make any new tool install requests based on that feedback.

Thanks and hope that gives you some options for now, Jen, Galaxy team

ADD COMMENTlink modified 6 weeks ago • written 6 weeks ago by Jennifer Hillman Jackson25k
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