Is anyone doing tertiary analysis of their DNASeq data?

DanFrost · 01-04-2012, 07:47 AM

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 · 01-04-2012, 10:25 AM

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 · 01-04-2012, 01:29 PM

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 · 01-05-2012, 09:53 AM

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 · 01-05-2012, 10:47 AM

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 · 01-10-2012, 12:02 PM

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

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01-04-2012, 07:47 AM	#1
DanFrost Member Location: Bozeman, MT Join Date: Dec 2011 Posts: 21	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

01-05-2012, 09:53 AM	#4
NextGenSeq Senior Member Location: USA Join Date: Apr 2009 Posts: 482	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 09:55 AM.

01-05-2012, 10:47 AM	#5
jjohnson Member Location: Washington DC Metro Area Join Date: Aug 2009 Posts: 20	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. __________________ Justin H. Johnson \| Twitter: @BioInfo \| LinkedIn: http://bit.ly/LIJHJ \| EdgeBio

01-04-2012, 10:25 AM	#2
adaptivegenome Super Moderator Location: US Join Date: Nov 2009 Posts: 437	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.

01-04-2012, 01:29 PM	#3
DanFrost Member Location: Bozeman, MT Join Date: Dec 2011 Posts: 21	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.

01-10-2012, 12:02 PM	#6
DanFrost Member Location: Bozeman, MT Join Date: Dec 2011 Posts: 21	Justin - thanks for the info. Full disclosure and funny coincidence - I work for Golden Helix!