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Question: Loss of original VCF file; therefore in Galaxy, can I use VCF manipulation on an excel file (originally converted from VCF format)
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gravatar for eleni.stylianou
9 months ago by
eleni.stylianou • 0
eleni.stylianou • 0 wrote:

I have inherited a project where the original VCF files were lost. I have the excel files derived from the VCF files for normal and tumor samples. I would like to compare the variants in these. Can I do this in Galaxy? I don't know of any variant manipulation packages that accept excel files.

convert excel vcf galaxy • 389 views
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modified 9 months ago by Jennifer Hillman Jackson ♦ 25k • written 9 months ago by eleni.stylianou • 0
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gravatar for Jennifer Hillman Jackson
9 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Converting the data back into VCF format would be the way to use the data analysis in Galaxy.

I don't know of any specific tools that automatically convert Excel-to-VCF. You are unlikely to find a script/command-line that would do this, without some tuning, as the format during the VCF-to-Excel transfer can be manipulated in many custom ways.

What you can do:

  • Exporting the data into tabular format would be the start.
  • Then try to manipulate it from tabular back into VCF format.
    • Review the data manipulation tools in Galaxy. Look in the Text manipulation and Datamash tool groups.
    • Edit the file yourself with a text editor, unix or other.
    • Search general bioinformatics websites for tips, shared scripts, etc.
    • The Galaxy Main Tool Shed https://usegalaxy.org/toolshed does have some tools for working with Excel data, but none do the operation you want. Search with the keyword "excel" to find/review these. If any do seem useful -- to you or others reading -- the tools are for use in your own Galaxy (not hosted at the public Galaxy Main https://usegalaxy.org site). https://galaxyproject.github.io/

FAQ that includes a link to the current VCF specification: https://galaxyproject.org/learn/datatypes/#vcf

Hope this works out! Jen, Galaxy team
ADD COMMENT • link modified 7 months ago • written 9 months ago by Jennifer Hillman Jackson ♦ 25k
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