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Question: Mpileup with vcf output?
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gravatar for marcelina.parra
6 weeks ago by
marcelina.parra • 0
marcelina.parra • 0 wrote:

Hello,

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 (https://samtools.github.io/bcftools/) and vcftools (https://vcftools.github.io/index.html) to Galaxy?
usegalaxy.* vcftools bcftools • 69 views
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modified 6 weeks ago by Jennifer Hillman Jackson ♦ 25k • written 6 weeks ago by marcelina.parra • 0
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gravatar for Jennifer Hillman Jackson
6 weeks ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

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
ADD COMMENT • link modified 6 weeks ago • written 6 weeks ago by Jennifer Hillman Jackson ♦ 25k
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