Question: Using Snpeff And Snpsift In Galaxy
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gravatar for shamsher jagat
4.6 years ago by
United States
shamsher jagat590 wrote:
I have a VCF file and I want to filter it for nonsynonymous/ deletion/ insertion seq variations. Once I filter this file and compare between tumor vs normal samples and then annotate such variations. I believe I can filter this file using SnpSift and then can annotate with SnpEff, When I try to use Snsift filter it just says arbitrary expression. Are there rules how to use expression for a particular filter with in galaxy. If any one has used SnpSift in galaxy may share their expertise. Thanks Kanwar
snpeff snp • 2.6k views
ADD COMMENTlink modified 4.6 years ago by Jennifer Hillman Jackson25k • written 4.6 years ago by shamsher jagat590
0
gravatar for Jennifer Hillman Jackson
4.6 years ago by
United States
Jennifer Hillman Jackson25k wrote:
Hi Kanwar, This tool in Galaxy uses the same expressions as the line command version (to my knowledge). A list of the possible expressions is listed here. The parenthesis are optional when there is just a single expression. http://snpeff.sourceforge.net/SnpSift.html#filter Hopefully this helps, Jen Galaxy team -- Jennifer Hillman-Jackson http://galaxyproject.org
ADD COMMENTlink written 4.6 years ago by Jennifer Hillman Jackson25k
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