VAT/download
From GersteinInfo
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# [http://www.gnu.org/software/gsl/ GSL] - GNU Scientific Library | # [http://www.gnu.org/software/gsl/ GSL] - GNU Scientific Library | ||
# [http://hgwdev.cse.ucsc.edu/~kent/exe/linux/blatSuite.34.zip BlatSuite] - BLAT and a collection of utility programs. Note these executables have to be part of the PATH. | # [http://hgwdev.cse.ucsc.edu/~kent/exe/linux/blatSuite.34.zip BlatSuite] - BLAT and a collection of utility programs. Note these executables have to be part of the PATH. | ||
| - | # [http://www.libgd.org/Main_Page GD library] | + | # [http://www.libgd.org/Main_Page GD library] - The GD library is used to create an image for each gene model and its associated variants. |
| - | # [http://samtools.sourceforge.net/tabix.shtml Tabix] is generic tool that indexes position-sorted files in tab-delimited formats to facilitate fast retrieval ([http://sourceforge.net/projects/samtools/files/tabix/ download]). | + | # [http://samtools.sourceforge.net/tabix.shtml Tabix] - Tabix is generic tool that indexes position-sorted files in tab-delimited formats to facilitate fast retrieval ([http://sourceforge.net/projects/samtools/files/tabix/ download]). |
| + | # [http://vcftools.sourceforge.net/index.html VCF tools] - VCF tools consists of a suite of useful modules to manipulate VCF files. | ||
<br> | <br> | ||
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=== Download === | === Download === | ||
| - | [http://archive.gersteinlab.org/proj/ | + | [http://archive.gersteinlab.org/proj/VAT VAT] suite consists of two components: |
| - | [http://archive.gersteinlab.org/proj/ | + | # [http://homes.gersteinlab.org/people/lh372/SOFT/bios/index.html BIOS], which is a general C library |
| + | # [http://archive.gersteinlab.org/proj/VAT VAT], which contains the Variant Annotation Tools | ||
==== Source code ==== | ==== Source code ==== | ||
| - | A TAR ball that contains the source code | + | A TAR ball that contains the source code can be downloaded here: |
| - | * [http://archive.gersteinlab.org/proj/ | + | * [http://archive.gersteinlab.org/proj/VAT/src VAT-0.5.tar.gz] - Initial upload |
| - | + | ||
| - | + | ||
==== Executables ==== | ==== Executables ==== | ||
Revision as of 15:52, 8 March 2011
Code
Required Software - External
- GSL - GNU Scientific Library
- BlatSuite - BLAT and a collection of utility programs. Note these executables have to be part of the PATH.
- GD library - The GD library is used to create an image for each gene model and its associated variants.
- Tabix - Tabix is generic tool that indexes position-sorted files in tab-delimited formats to facilitate fast retrieval (download).
- VCF tools - VCF tools consists of a suite of useful modules to manipulate VCF files.
Download
VAT suite consists of two components:
# BIOS, which is a general C library # VAT, which contains the Variant Annotation Tools
Source code
A TAR ball that contains the source code can be downloaded here:
- VAT-0.5.tar.gz - Initial upload
Executables
Statically built binaries for UNIX can be found here:
- RSEQtools-0.6_UNIX.tar.gz - 64bit version, last updated on 11/05/2010
Important Note ============== THIS PACKAGE (RSEQtools including BIOS and MRF) 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.
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.
