Dependences

The following packages are required by VAT:

  • GNU Scientific Library (GSL) - version-1.14; required for libBIOS, which is a general C library
  • GD library - The GD library is used to create an image for each gene model and its associated variants (version-2.0.35; required by VAT).
  • Tabix - Tabix (version-0.2.3) is a generic tool that indexes position-sorted files in tab-delimited formats to facilitate fast retrieval (download). These tools are utilized by VAT. Note: these executables must be part of the PATH.
  • BlatSuite - BLAT and a collection of utility programs. These tools are utilized by VAT. Note: these executables must be part of the PATH.
  • BIOS library - VAT uses a generic C library called BIOS (version-1.0.0)

The following are optional for the VAT pipeline but required for some additional functionality:

  • VCF Tools - VCF tools consists of a suite of useful modules to manipulate VCF files.

VAT Download

Note

THIS PACKAGE (VAT) IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESSED OR IMPLIED WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.

Source code

A tarball of the source code of the Variant Annotation Tool may be download here. Version 2.0.1 contains the new VAT web components.

Executables

Tarballs containing statically built binaries for 64-bit Linux Red Hat can be downloaded here:

License information

The software package is released under the Creative Commons license (Attribution-NonCommerical)

For more details please refer to the Permissions Page on the Gerstein Lab webpage.

Preprocessed GENCODE annotation sets

The following annotation sets are derived from the GENCODE project. Each each entry has a set of transcript coordinates (in Interval format) and a set of transcript sequences (introns removed; sequence with respect to the '+' strand; in FASTA format). These annotation files may also be obtained by running the script get_annotation_sets.sh included in the VAT source distribution.

Coding sequence (CDS) elements where the both the gene_type and transcript_type are protein_coding:

GENCODE version 3b (hg18) Transcript coordinates Transcript sequences
GENCODE version 3c (hg19) Transcript coordinates Transcript sequences
GENCODE version 4 (hg19) Transcript coordinates Transcript sequences
GENCODE version 5 (hg19) Transcript coordinates Transcript sequences
GENCODE version 6 (hg19) Transcript coordinates Transcript sequences
GENCODE version 7 (hg19) Transcript coordinates Transcript sequences