e765272cce5886370af96fd8dc507cb4e5373964 steve Mon Dec 19 15:17:46 2011 -0800 Added VCF announcement diff --git src/hg/htdocs/indexNews.html src/hg/htdocs/indexNews.html index 7139746..bb905a6 100644 --- src/hg/htdocs/indexNews.html +++ src/hg/htdocs/indexNews.html @@ -1,110 +1,129 @@
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+ 19 December 2011 - Variant + Call Format (VCF) Now Supported in Genome Browser +

+ We are pleased to announce that the UCSC Genome Browser + now supports Variant Call Format (VCF). VCF is a flexible + and extendable line-oriented text format developed by the + 1000 Genomes Project for releases of single nucleotide variants, + indels, copy number variants and structural variants discovered + by the project. Similar to bigBed, bigWig and BAM, the Browser + transfers only the portions of VCF files necessary to display + viewed regions, making VCF a fast and attractive option for + large data sets. VCF files will need to be compressed and + indexed using the tabix package available from + SAMtools. This new format is available + for use in custom tracks and data hubs. For more information + about VCF and tabix, please see our VCF Track Format help page.

+

7 November 2011 - UMD Cow Assembly Now Available in Genome Browser

In response to the many requests from the bovine research community, we now offer the University of Maryland (UMD) Bos taurus assembly in the Genome Browser, in addition to the assemblies produced by the Baylor College of Medicine Human Genome Sequencing Center. The UMD v3.1 assembly (Nov. 2009, UCSC bosTau6) was produced by the UMD Center for Bioinformatics and Computational Biology (CBCB) in College Park, MD.

The UMD 3.1 assembly is based on reads downloaded from the NCBI Trace Archive, most of which were sequenced by the Baylor College of Medicine. UMD reports that they were able to apply several assembly improvement techniques to produce an assembly that is substantially more accurate and complete than previous alternative versions, as evaluated using independent metrics. Based on UMD statistics, this assembly provides more genome coverage, closes thousands of gaps, corrects many erroneous inversions, deletions, and translocations, and fixes thousands of single-nucleotide errors. For more information, see Zimin AV et al, A whole-genome assembly of the domestic cow, Bos taurus, Genome Biol. 2009;10(4) and the UMD CBCB Bos taurus assembly web page.

Downloads of the UMD bovine data and annotations may be obtained from the UCSC Genome Browser FTP server or Downloads page.

We'd like to thank the UMD CBCB for providing this genome assembly. The UMD Cow Genome Browser and annotation tracks were produced by Hiram Clawson, Chin Li, Brooke Rhead, Greg Roe, Steve Heitner, and Donna Karolchik. See the Credits page for a detailed list of the organizations and individuals who contributed to this release.

10 October 2011 - Updated Yeast Browser Released: We are happy to announce the release of an updated browser for the Saccharomyces cerevisiae yeast genome. Read more.

8 September 2011 - New Navigation and Display Features: We've added several new features to the Genome Browser that make it easier to quickly configure and navigate around in the browser's annotation tracks window. Read more.

18 August 2011 - New Feature: Track Data Hubs: We are pleased to announce a new feature in the UCSC Genome Browser: Track Data Hubs. Track hubs are web-accessible directories of genomic data that can be viewed on the UCSC Genome Browser alongside native annotation tracks. Read more.

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