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Bioinformatics. 2016 May 1;32(9):1430-2. doi: 10.1093/bioinformatics/btv766. Epub 2016 Jan 6.

UCSC Data Integrator and Variant Annotation Integrator.

Author information

1
Genomics Institute, University of California, Santa Cruz, CA, USA.
2
Computational Biology Graduate Group, University of California, Berkeley, CA, USA and.
3
Genomics Institute, University of California, Santa Cruz, CA, USA, Howard Hughes Medical Institute, University of California, Santa Cruz, CA, USA.

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.

PMID:
26740527
PMCID:
PMC4848401
DOI:
10.1093/bioinformatics/btv766
[Indexed for MEDLINE]
Free PMC Article

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