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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