Hi Laura,

Before running the filter tool, save the header off into a separate dataset using the tool "Text Manipulation -> Select first lines from a dataset". Then, after filtering, add the header back on with the tool "Concatenate datasets tail-to-head" listing the header-only dataset first and the filtered dataset second.


If you need to reassign the datatype as well, click on the 'pencil" icon in the final result dataset to reach the "Edit Attributes" form, scroll down to the section 'Change data type', assign, and save.

Hopefully this helps,

Jen
Galaxy team

On 5/7/12 8:47 AM, Laura Reinholdt wrote:
I’m using a local instance of Galaxy. I’d like to filter a VCF file for
SNPs that have passed filter (as indicated in the VCF file as “PASS”
under column 7, FILTER). I can use the basic tab file filter tool
(c7==’PASS’), but the resulting file has lost the VCF header and that’s
causing a problem with the annotation tool that I want to use. Any
advice on how to get around this?

Thanks,

Laura


Laura Reinholdt, PhD
Research Scientist
Genetic Resource Science
The Jackson Laboratory
600 Main Street
Bar Harbor, ME 04609-1500
(207) 288-6000, ext. 6693

_http://research.jax.org/grs/
http://research.jax.org/faculty/laura-reinholdt.html
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