Atlas2

About the Software

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

Atlas2 is a next-generation sequencing 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 versions 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

• Unix-like operation systems

• Ruby 1.9.1: http://www.ruby-lang.org/en/downloads/

• If you do not have a 64-bit Linux system, a C++ compiler and Make must be installed

• If needed, the external mapping tools—BLAT and cross_match—can be obtained from http://users.soe.ucsc.edu/~kent/src/ and http://www.phrap.org respectively.

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

Download

Current release

Version 1.4.3 (01-03-2013)

Version 1.4.3 software and documentation at SourceForge

Previous releases

Version 1.4.1 (09-10-2012)

Version 1.4.1 software and documentation at SourceForge

Version 1.0 (08-29-2011)

Version 1.0 software and documentation at SourceForge

License

Copyright (c) 2011, Human Genome Sequencing Center, Baylor College of Medicine. All rights reserved.

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.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE

Publications

Challis D. etc. An integrative variant analysis suite for whole exome next-generation sequencing data. BMC Bioinformatics 2012, 13:8 doi:10.1186/1471-2105-13-8

Contact

For additional information, contact Danny Challis, Jin Yu, and Fuli Yu.

Release History