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Old 01-12-2011, 10:21 AM   #1
mrxcm3
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Location: Nottingham

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Default Softwear to visualise snps called from NGS

I used DeepSeq to identify novel SNPs in targeted amplicon regions. I have annotated these SNPs using variant classifier. However, I am yet to find a tool that can graphically display these SNPs in their genomic context. I was wondering if their is a stand alone tool, or perhaps something as part of a pipeline programme i can tap into? Anyone know of any?
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Old 01-13-2011, 02:07 AM   #2
doc.ramses
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You can use custom tracks in the UCSC Genome Browser. http://genome.ucsc.edu/index.html
You can also setup a local installation of this, if you prefer this.
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Old 01-13-2011, 11:56 AM   #3
maubp
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Not my field, but is Flapjack relevant?
http://bioinf.scri.ac.uk/flapjack/
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Old 01-14-2011, 12:25 PM   #4
Jean
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I really like the Integrative Genomics Browser lately:
http://www.broadinstitute.org/software/igv/
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