Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2016 May 1;32(9):1430-2.
doi: 10.1093/bioinformatics/btv766. Epub 2016 Jan 6.

UCSC Data Integrator and Variant Annotation Integrator

Affiliations
Free PMC article

UCSC Data Integrator and Variant Annotation Integrator

Angie S Hinrichs et al. Bioinformatics. .
Free PMC article

Abstract

Two new tools on the UCSC Genome Browser web site provide improved ways of combining information from multiple datasets, optionally including the user's own custom track data and/or data from track hubs. The Data Integrator combines columns from multiple data tracks, showing all items from the first track along with overlapping items from the other tracks. The Variant Annotation Integrator is tailored to adding functional annotations to variant calls; it offers a more restricted set of underlying data tracks but adds predictions of each variant's consequences for any overlapping or nearby gene transcript. When available, it optionally adds additional annotations including effect prediction scores from dbNSFP for missense mutations, ENCODE regulatory summary tracks and conservation scores.

Availability and implementation: The web tools are freely available at http://genome.ucsc.edu/ and the underlying database is available for download at http://hgdownload.cse.ucsc.edu/ The software (written in C and Javascript) is available from https://genome-store.ucsc.edu/ and is freely available for academic and non-profit usage; commercial users must obtain a license.

Contact: angie@soe.ucsc.edu

Supplementary information: Supplementary data are available at Bioinformatics online.

Similar articles

  • Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser.
    Raney BJ, Dreszer TR, Barber GP, Clawson H, Fujita PA, Wang T, Nguyen N, Paten B, Zweig AS, Karolchik D, Kent WJ. Raney BJ, et al. Bioinformatics. 2014 Apr 1;30(7):1003-5. doi: 10.1093/bioinformatics/btt637. Epub 2013 Nov 13. Bioinformatics. 2014. PMID: 24227676 Free PMC article.
  • The UCSC Genome Browser database: 2014 update.
    Karolchik D, Barber GP, Casper J, Clawson H, Cline MS, Diekhans M, Dreszer TR, Fujita PA, Guruvadoo L, Haeussler M, Harte RA, Heitner S, Hinrichs AS, Learned K, Lee BT, Li CH, Raney BJ, Rhead B, Rosenbloom KR, Sloan CA, Speir ML, Zweig AS, Haussler D, Kuhn RM, Kent WJ. Karolchik D, et al. Nucleic Acids Res. 2014 Jan;42(Database issue):D764-70. doi: 10.1093/nar/gkt1168. Epub 2013 Nov 21. Nucleic Acids Res. 2014. PMID: 24270787 Free PMC article.
  • Navigating protected genomics data with UCSC Genome Browser in a Box.
    Haeussler M, Raney BJ, Hinrichs AS, Clawson H, Zweig AS, Karolchik D, Casper J, Speir ML, Haussler D, Kent WJ. Haeussler M, et al. Bioinformatics. 2015 Mar 1;31(5):764-6. doi: 10.1093/bioinformatics/btu712. Epub 2014 Oct 27. Bioinformatics. 2015. PMID: 25348212 Free PMC article.
  • UCSC genome browser tutorial.
    Zweig AS, Karolchik D, Kuhn RM, Haussler D, Kent WJ. Zweig AS, et al. Genomics. 2008 Aug;92(2):75-84. doi: 10.1016/j.ygeno.2008.02.003. Epub 2008 Jun 2. Genomics. 2008. PMID: 18514479 Review.
  • Mitochondrial Disease Sequence Data Resource (MSeqDR): a global grass-roots consortium to facilitate deposition, curation, annotation, and integrated analysis of genomic data for the mitochondrial disease clinical and research communities.
    Falk MJ, Shen L, Gonzalez M, Leipzig J, Lott MT, Stassen AP, Diroma MA, Navarro-Gomez D, Yeske P, Bai R, Boles RG, Brilhante V, Ralph D, DaRe JT, Shelton R, Terry SF, Zhang Z, Copeland WC, van Oven M, Prokisch H, Wallace DC, Attimonelli M, Krotoski D, Zuchner S, Gai X; MSeqDR Consortium Participants; MSeqDR Consortium participants: Sherri Bale, Jirair Bedoyan, Doron Behar, Penelope Bonnen, Lisa Brooks, Claudia Calabrese, Sarah Calvo, Patrick Chinnery, John Christodoulou, Deanna Church,; Rosanna Clima, Bruce H. Cohen, Richard G. Cotton, IFM de Coo, Olga Derbenevoa, Johan T. den Dunnen, David Dimmock, Gregory Enns, Giuseppe Gasparre,; Amy Goldstein, Iris Gonzalez, Katrina Gwinn, Sihoun Hahn, Richard H. Haas, Hakon Hakonarson, Michio Hirano, Douglas Kerr, Dong Li, Maria Lvova, Finley Macrae, Donna Maglott, Elizabeth McCormick, Grant Mitchell, Vamsi K. Mootha, Yasushi Okazaki,; Aurora Pujol, Melissa Parisi, Juan Carlos Perin, Eric A. Pierce, Vincent Procaccio, Shamima Rahman, Honey Reddi, Heidi Rehm, Erin Riggs, Richard Rodenburg, Yaffa Rubinstein, Russell Saneto, Mariangela Santorsola, Curt Scharfe,; Claire Sheldon, Eric A. Shoubridge, Domenico Simone, Bert Smeets, Jan A. Smeitink, Christine Stanley, Anu Suomalainen, Mark Tarnopolsky, Isabelle Thiffault, David R. Thorburn, Johan Van Hove, Lynne Wolfe, and Lee-Jun Wong. Falk MJ, et al. Mol Genet Metab. 2015 Mar;114(3):388-96. doi: 10.1016/j.ymgme.2014.11.016. Epub 2014 Dec 4. Mol Genet Metab. 2015. PMID: 25542617 Free PMC article. Review.
See all similar articles

Cited by 16 articles

See all "Cited by" articles

References

    1. Cingolani P. et al. (2012) A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly (Austin), 6, 80–92. - PMC - PubMed
    1. Danecek P. et al. (2011) The variant call format and VCFtools. Bioinformatics, 27, 2156–2158. - PMC - PubMed
    1. Eilbeck K. et al. (2005) The Sequence Ontology: a tool for the unification of genome annotations. Genome Biol., 6, R44. - PMC - PubMed
    1. Karolchik D. et al. (2003) The UCSC Genome browser database. Nucleic Acids Res., 31, 51–54. - PMC - PubMed
    1. Karolchik D. et al. (2004) The UCSC table browser data retrieval tool. Nucleic Acids Res., 32, D493–D496. - PMC - PubMed
Feedback