Question: Loss of original VCF file; therefore in Galaxy, can I use VCF manipulation on an excel file (originally converted from VCF format)
gravatar for eleni.stylianou
18 days ago by
eleni.stylianou0 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 excell vcf galaxy • 57 views
ADD COMMENTlink modified 18 days ago by Jennifer Hillman Jackson24k • written 18 days ago by eleni.stylianou0
gravatar for Jennifer Hillman Jackson
18 days ago by
United States
Jennifer Hillman Jackson24k wrote:


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 Excell-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-Excell 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.

FAQ that includes a link to the current VCF specification:

Hope this works out! Jen, Galaxy team

ADD COMMENTlink written 18 days ago by Jennifer Hillman Jackson24k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 75 users visited in the last hour