Tuesday, 20 December 2011
UCSC Genome Browser now supports Variant Call Format (VCF)
I just received this interesting email from the UCSC Genome Bioinformatics Group (see below). The official support of the Variant Call Format will allow to displays within the UCSC Genome browser window variant base calls from the data generated from your lab as well as from several personal genomes that have been made publicly available.
From: Steve Heitner
Subject: [Genome-announce] New Variant Call Format (VCF) support
Date: 19 dicembre 2011 23:58:16 GMT+01:00
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 http://samtools.sourceforge.net/. 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 at http://genome.ucsc.edu/goldenPath/help/vcf.html.
UCSC Genome Bioinformatics Group