VAT

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		+	== Introduction ==
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		+	The Variant Annotation Tool (VAT) consists of a set of modules to annotate genetic variants including SNPs and Indels. Furthermore, this suite also contains a program to aggregate SNP and indel variants at the gene level and generate an image to visualize the genetic 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 will also integrate allele frequencies and genotype data providing population-specific information from published high quality variation databases such as Hapmap and 1000 genomes.
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Revision as of 17:33, 6 March 2011

VAT Main Page

Contents 1 Introduction 2 Data formats 2.1 Variant Call Format (VCF) 2.2 Interval Format

Introduction

The Variant Annotation Tool (VAT) consists of a set of modules to annotate genetic variants including SNPs and Indels. Furthermore, this suite also contains a program to aggregate SNP and indel variants at the gene level and generate an image to visualize the genetic 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 will also integrate allele frequencies and genotype data providing population-specific information from published high quality variation databases such as Hapmap and 1000 genomes.

Data formats

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Variant Call Format (VCF)

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.