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Question: Conversion of a .vcf (variant control format) to a .maf (mutation annotation file)
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7 months ago by
galaxyNewbie • 30
galaxyNewbie • 30 wrote:

Hello, Is there a galaxy package which will convert a .vcf to a .maf (mutation annotation file)? I didn't see vcf2maf as an available package.

Thank you.
development vcf2maf maftools vcf maf • 667 views
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modified 7 months ago by Jennifer Hillman Jackson ♦ 25k • written 7 months ago by galaxyNewbie • 30
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gravatar for Jennifer Hillman Jackson
7 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

These tools have not been wrapped for Galaxy yet (at least not publically), but they could be.

Reference: https://bioconductor.org/packages/3.7/bioc/vignettes/maftools/inst/doc/maftools.html

Choices:

  1. Wrap the tool (or tools) yourself and submit them to the ToolShed. Use Planemo for development/tests/publication: http://planemo.readthedocs.io/en/latest/
  2. Submit an enhancement issue ticket to the IUC (https://galaxyproject.org/iuc/) for these to be considered for a new development project. This could be combined with (1) above -- many tool wrappers are developed in collaboration. https://github.com/galaxyproject/tools-iuc/issues
  3. Follow up on my post at the IUC Gitter channel here asking about development plans (if any) for this tool suite: https://gitter.im/galaxy-iuc/iuc?at=5adf8eb1270d7d37080095b1

Thanks! Jen, Galaxy team
ADD COMMENT • link modified 7 months ago • written 7 months ago by Jennifer Hillman Jackson ♦ 25k
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