Question: Using Snpeff And Snpsift In Galaxy
gravatar for shamsher jagat
4.5 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 • 2.5k views
ADD COMMENTlink modified 4.5 years ago by Jennifer Hillman Jackson25k • written 4.5 years ago by shamsher jagat590
gravatar for Jennifer Hillman Jackson
4.5 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. Hopefully this helps, Jen Galaxy team -- Jennifer Hillman-Jackson
ADD COMMENTlink written 4.5 years ago by Jennifer Hillman Jackson25k
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