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Old 01-04-2012, 06:47 AM   #1
DanFrost
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Lightbulb Is anyone doing tertiary analysis of their DNASeq data?

Hello!

I am new here and just trying to get a sense of what everyone is up to. From reading through pages and pages of this forum, I noticed that I didn't see a lot of threads about the statistical analysis or classification of DNA Seq variants.

Anyone out there doing this kind of work?



Cheers,

Dan
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Old 01-04-2012, 09:25 AM   #2
adaptivegenome
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Moved to "General" since this is not a specific question. And yes, many people on the board actively debate the best way to identify true variation from errors arising from sequencing, mapping, etc.
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Old 01-04-2012, 12:29 PM   #3
DanFrost
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Ahh, thank you so much for moving this to the proper place.

I have experience with collapsing methods for both common and rare variant burden, but not much outside of that for statistical analysis of variant results.
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Old 01-05-2012, 08:53 AM   #4
NextGenSeq
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For determining whether a novel SNP is a potential mutation PolyPhen is pretty good

http://genetics.bwh.harvard.edu/pph/

http://genetics.bwh.harvard.edu/pph2/

Last edited by NextGenSeq; 01-05-2012 at 08:55 AM.
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Old 01-05-2012, 09:47 AM   #5
jjohnson
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We use several tools to call, classify, assign confidence, and annotate. A good place to start is the GATK website. The GATK calls and integrates variant annotation via SNPEff as well as provides a wealth of info per SNP to help you ascribe a confidence to the call. For comparative analysis we have looked into PLINK/SEQ from Harvard and Goldenhelix (Commercial), and other popular tools for annotation are annovar and Variant Effect predictor from ENSEMBL. In addition to PolyPhen, SIFT is a nice tool/database as well.
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Old 01-10-2012, 11:02 AM   #6
DanFrost
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Justin - thanks for the info. Full disclosure and funny coincidence - I work for Golden Helix!
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