VAT
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== Introduction == | == Introduction == | ||
- | The Variant Annotation Tool (VAT) consists of a set of modules to annotate genetic variants including SNPs and Indels. | + | The Variant Annotation Tool (VAT) consists of a set of modules to annotate genetic variants including SNPs and Indels. This software package also contains a program to aggregate SNP and indel variants at the gene level. Subsequently, an image is generated to visualize the functional impact of these variants on the gene models. This information can then be viewed and shared using a web-interface. In addition to annotation of the coding variants, this tool also integrates allele frequencies and genotype data providing population-specific information from published high quality variation databases such as [http://www.1000genomes.org 1000 Genomes Project]. |
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Revision as of 17:57, 6 March 2011
Contents |
Introduction
The Variant Annotation Tool (VAT) consists of a set of modules to annotate genetic variants including SNPs and Indels. This software package also contains a program to aggregate SNP and indel variants at the gene level. Subsequently, an image is generated to visualize the functional impact of these variants on the gene models. This information can then be viewed and shared using a web-interface. In addition to annotation of the coding variants, this tool also integrates allele frequencies and genotype data providing population-specific information from published high quality variation databases such as 1000 Genomes Project.
Data formats
Variant Call Format (VCF)
The Variant Call Format (VCF) is a tab-delimited text file format to represent a number of different genetic variants including SNPs and Indels. It was developed as part of the 1000 Genomes Project.
Interval Format
The Interval format consists of eight tab-delimited columns and is used to represent genomic intervals such as genes. This format is closely associated with the intervalFind module, which is part of BIOS. This module efficiently finds intervals that overlap with a query interval. The underlying algorithm is based on containment sublists: Alekseyenko, A.V., Lee, C.J. "Nested Containment List (NCList): A new algorithm for accelerating interval query of genome alignment and interval databases" Bioinformatics 2007;23:1386-1393 [1].
1. Name of the interval 2. Chromosome 3. Strand 4. Interval start (with respect to the "+") 5. Interval end (with respect to the "+") 6. Number of sub-intervals 7. Sub-interval starts (with respect to the "+", comma-delimited) 8. Sub-interval end (with respect to the "+", comma-delimited)
Example file:
uc001aaw.1 chr1 + 357521 358460 1 357521 358460 uc001aax.1 chr1 + 410068 411702 3 410068,410854,411258 410159,411121,411702 uc001aay.1 chr1 - 552622 554252 3 552622,553203,554161 553066,553466,554252 uc001aaz.1 chr1 + 556324 557910 1 556324 557910 uc001aba.1 chr1 + 558011 558705 1 558011 558705
In this example the intervals represent a transcripts, while the sub-intervals denote exons.
Note: the coordinates in the Interval format are zero-based and the end coordinate is not included.