About the Software

Authors: Jin Yu, Yufeng Shen, Cristian Coarfa and Fuli Yu

© Baylor College of Medicine Human Genome Sequencing Center. All rights reserved.

Atlas-SNP2 is a SNP discovery tool developed for next generation sequencing platforms such as Roche 454 and Illumina. It is implemented in Ruby at HGSC.

System Requirements

• Unix-like operation systems
• Ruby 1.9.x: 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 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.

License

This software is free for all uses with the following restrictions:

• No part of this software, or modifications thereof, may be redistributed for any purpose to any other company, person, or individual, without prior written permission from the author.
• This software is provided AS IS. Baylor College of Medicine assumes no responsibility or liability for damages of any kind that may result, directly or indirectly, from the use of this software.
• The above copyright notice must be preserved in the executable About dialog or made visible to users in some other way.

Download

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

Current release: Version 1.2 (01-18-2011)

• Version 1.2 software

Previous releases

Version 1.1 (04-26-2010):

• Version 1.1 software
• Version 1.1 documentation

Version 1.0 (01-20-2010):

• Version 1.0 software
• Version 1.0 documentation

Version 0.1 (12-10-2009):

• Version 0.1 software

Release History

What's new in version 1.2 (01-18-2011):

Version 1.2 is a major upgrade of Atlas-SNP2

New features

• one-stop running: take sorted BAM files and reference file as input and output SNP genotypes in VCF format
• use mapping quality score as alignment quality control
• use insertion size as mapping quality control for pair-end re-sequencing data
• more filters are integrated for higher quality SNP calls

Performance

• whole genome SNP calling is doable on a typical PC with 4G memory now. In our test, it can process 1 million reads per 5 minutes for whole exome SNP calling only using one CPU core of Xeon 5520 and 4G memory

Bugs fixed and compatibility

• more robust to alignment errors
• crossmatch2SAM tool is compatible to Ruby 1.9.X now
• a few minor bugs

Version 1.1 (04-26-2010):

• added a heuristics-based genotyping module
• added a column of “numRefReads_afterFilter” in Atlas-SNP2 result file
• revised the header line in Atlas-SNP2 output file to be more explicit
• skipped duplicate reads masked in the BAM files when processing
• added an option for the user to setup the max number of alignments allowed to be piled up at a particular site
• printed more running information and more detailed alignments statistics
• more robust to various alignments errors
• fixed several bugs

Version 1.0 (01-20-2010):

• added Illumina Platform support
• all calculations are now based on required fields of SAM to get maximum compatibility
• added CIGAR and reference sequence test code
• used pileup number to calculate TotalCoverage
• improved performance
• migrated to Ruby 1.9
• many minor improvements

Draft release version 0.1 (12-10-2009):

• initial implementation
• initial support of SAM files

Contact

For additional information, contact Jin Yu at jy2@bcm.edu and Fuli Yu at fyu@bcm.edu.