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 The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.
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 _
The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.
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