View source for BoG2012VariationPoster

This page contains links related to the UCSC Genome Browser poster presented by [[User:AngieHinrichs|Angie]] at Biology of Genomes 2012 [http://meetings.cshl.edu/meetings/genome12.shtml])

=Poster: Using the UCSC Genome Browser to evaluate putative genetic variants=

* Files: [[Media:Hinrichs_BoG2012_GBVariants.pptx|.pptx]], [[Media:Hinrichs_BoG2012_GBVariants.pdf|PDF]]

==View poster screenshots in the Genome Browser==

* [http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=AngieHinrichs&hgS_otherUserSessionName=BoG.2012.commonOmimAV Is there an associated phenotype?]
* [http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=AngieHinrichs&hgS_otherUserSessionName=BoG.2012.PramefCommonDel How rare is this deletion?]
* [http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=AngieHinrichs&hgS_otherUserSessionName=BoG.2012.fictionalVarPseudogeneRegPeak Novel variant: what's in the neighborhood?]
* [http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=AngieHinrichs&hgS_otherUserSessionName=BoG.2012.funWith1kG Decoding the VCF w/phased genotypes display]
* [http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=AngieHinrichs&hgS_otherUserSessionName=BoG.2012.dbSNPbabyBathwater dbSNP: Not just polymorphisms]

==1000 Genomes Phase 1 v3 integrated variants (May 2012) used in the poster==
Thanks to the [http://www.1000genomes.org/ 1000 Genomes Project] for making these data available:
[ftp://ftp.ncbi.nih.gov/1000genomes/ftp/release/20110521/ ftp://ftp.ncbi.nih.gov/1000genomes/ftp/release/20110521/]
To view a chromosome's phased genotype calls in the browser, right-click to copy the corresponding link ending in ".genotypes.vcf.gz" and then use that as the bigDataUrl parameter as described here: [http://genome.ucsc.edu/goldenPath/help/vcf.html http://genome.ucsc.edu/goldenPath/help/vcf.html]

==How to get help==
* Search for answers in our mail list archives: [http://genome.ucsc.edu/contacts.html http://genome.ucsc.edu/contacts.html]
* Email a new question to our actively monitored list [mailto:genome@soe.ucsc.edu genome@soe.ucsc.edu]
* OpenHelix's free training materials: [http://www.openhelix.com/downloads/ucsc/ucsc_home.shtml http://www.openhelix.com/downloads/ucsc/ucsc_home.shtml]

==Other posters about the UCSC Genome Browser==

* Visually integrating genomic data in the UCSC Genome Browser. Hinrichs AS ''et al.'' HGV 2011 [[HGV2011|genomewiki page]]  [[Media:HGV2011_GenomeBrowser.pptx|.pptx]], [[Media:HGV2011_GenomeBrowser.pdf|PDF]]
* UCSC Genome Browser Data Hubs. Zweig AS ''et al.'' Biology of Genomes, 2011 [http://users.soe.ucsc.edu/~ann/BoG2011.pdf PDF]
* Genome-wide ENCODE Data at UCSC. Rosenbloom KR ''et al.'' ASHG, 2010. [[Media:ENCODE_ASHG2010.ppt|PPT]]
* UCSC Genome Browser Tool Suite. Hinrichs AS ''et al.'' Genomics of Common Disease, 2008: [[Media:UCSC_Genome_Browser_GCD_2008.ppt|.ppt]], [[Media:UCSC_Genome_Browser_GCD_2008.pdf|PDF]]