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Question: Script of VCF4.1 parser (or VCF4.1 *xml).
1
gravatar for priyal
4.0 years ago by
priyal • 10
United Kingdom
priyal • 10 wrote:

Hi,

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.

Thanks.

PDZ 
galaxy samtools • 506 views
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modified 4.0 years ago by Jennifer Hillman Jackson ♦ 25k • written 4.0 years ago by priyal • 10
0
gravatar for Jennifer Hillman Jackson
4.0 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

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.
http://getgalaxy.org
http://usegalaxy.org/toolshed

The alternative is to use the public Main Galaxy instance at http://usegalaxy.org, 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).
http://wiki.galaxyproject.org/Support#Custom_reference_genome

Thanks, Jen, Galaxy team
ADD COMMENT • link written 4.0 years ago by Jennifer Hillman Jackson ♦ 25k
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