Is anyone doing tertiary analysis of their DNASeq data?

[DanFrost]

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

[adaptivegenome]

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.

[DanFrost]

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.

[NextGenSeq]

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/

[jjohnson]

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.

[DanFrost]

Justin - thanks for the info. Full disclosure and funny coincidence - I work for Golden Helix!