Question: Script of VCF4.1 parser (or VCF4.1 *xml).
gravatar for priyal
4.0 years ago by
United Kingdom
priyal10 wrote:


Does anyone have a python script to parse a VCF4.1 format.  I would like to modify it to parse manta output that we are getting.



galaxy samtools • 506 views
ADD COMMENTlink modified 4.0 years ago by Jennifer Hillman Jackson25k • written 4.0 years ago by priyal10
gravatar for Jennifer Hillman Jackson
4.0 years ago by
United States
Jennifer Hillman Jackson25k wrote:


All of the vcf tool wrappers for Galaxy are available in the tool shed. Many are python based, or the underlying 3rd party tool executed by a python wrapper.You can run most wrappers command-line without too much trouble. Run it in Galaxy first, then review the command-line on the "i" info page if you are not sure how build that up. A local will be needed, but you don't have to fully "productionalize it", just the basics at the top of the wiki.

The alternative is to use the public Main Galaxy instance at, add your genome as a "Custom Reference Genome" , complete with creating the "Custom Build" and assigning that to datasets. A custom build allows you to use the tools that interpret the "database" attribute when executing (not all forms have options to use a Custom Genome and include datasets from your history directly). But combined, this does permit use in most cases (not all tools, but most).

Thanks, Jen, Galaxy team

ADD COMMENTlink written 4.0 years ago by Jennifer Hillman Jackson25k
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