Question: Conversion of a .vcf (variant control format) to a .maf (mutation annotation file)
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gravatar for galaxyNewbie
27 days ago by
galaxyNewbie10
galaxyNewbie10 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.

ADD COMMENTlink modified 27 days ago by Jennifer Hillman Jackson25k • written 27 days ago by galaxyNewbie10
0
gravatar for Jennifer Hillman Jackson
27 days ago by
United States
Jennifer Hillman Jackson25k 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 COMMENTlink modified 27 days ago • written 27 days ago by Jennifer Hillman Jackson25k
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