HGSC at Baylor College of Medicine

About the Software

Authors: Danny Challis, Jin Yu, Uday Evani, and Fuli Yu

Atlas2 is a suite of variant analysis tools specializing in the separation of true SNPs and insertions and deletions (indels) from sequencing and mapping errors in Whole Exome Capture Sequencing (WECS) data. SNPs may be called using the Atlas-SNP2 application and indels may be called using the Atlas-Indel2 application. The suite implements logistic regression models trained on validated WECS data to identify the true variants. There is a separate regression model for each sequencing platform. The suite currently supports the SOLiD, Illumina, and Roche 454 (SNPs only) platforms. Future version of Atlas2 will include additional models for new sequencing platforms.

The Atlas2 suite takes a Binary sequence Alignment/Mapping (BAM) file (see http://samtools.sourceforge.net/SAM1.pdf) and a FASTA reference genome as input and produces variant calls in Variant Call Format (VCF) (see http://www.1000genomes.org/wiki/Analysis/vcf4.0). In addition to variant calls, the application collects coverage information and uses simple heuristic cutoffs to estimate the likely genotype of each variant site.

System Requirements and Installation

Unix-like operation systems
Ruby 1.9.1: http://www.ruby-lang.org/en/downloads/
SAMtools must be installed and runnable by invoking the "samtools" command
-SAMtools may be obtained at http://samtools.sourceforge.net/
If you do not have a 64-bit Linux system, a C++ compiler and Make must be installed

SOLiD-SNP-caller is coded in C++ and must be compiled to run. For 64-bit Linux system this has already been done. If you have a different system take the following steps before running SOLiD-SNP-caller for the first time:

Navigate to the SOLiD-SNP-caller directory in a terminal
Run: make clean
Run: make
Compiling may take several minutes

License

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.

Download

By downloading this software you explicitly agree to the license terms above.

Current release: Atlas2

Version 1.0 (08-29-2011):

Version 1.0 software
Version 1.0 documentation
For the application wiki and the latest development code, please visit sourceforge.

Previous release: Atlas-Indel2

Version 0.2 (02-09-2011):

Version 0.1 (12-2010):

Previous release: Atlas-SNP2

Version 1.1 (04-26-2010):

Version 1.0 (01-20-2010):

Version 0.1 (12-10-2009):

Version 0.1 software

Contact

For additional information, contact Danny Challis (challis@bcm.edu), Jin Yu (Evani@bcm.edu), Uday Evani (Evani@bcm.edu), and Fuli Yu (fyu@bcm.edu).