Atlas2 Suite

Introduction

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 Sequecing (WECS) data. The suite currently supports the SOLiD, Illumina, and Roche 454 (SNPs only) platforms. Future version of Atlas2 will include additional models for newer sequencing platforms.

The Atlas2 suite takes a Binary sequence Alignment/Mapping (BAM) file and a FASTA reference genome as input and produces variant calls in Variant Call Format (VCF). In addition to variant calls, the application collects coverage information and uses simple heuristic cutoffs to estimate the likely genotype of each variant site.

Please refer to the BMC Bioinformatics and Genome Research publications for more detailed information on the tool.

System Requirements

• Unix-like operation system
• 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/

Preprocessing

Although Atlas2 will function on any sorted BAM file, there are number of preprocessing steps that we recommend for the highest quality results.

• Mark or remove PCR duplicates using PicardMarkDuplicates or a similar tool.
• Base quality recalibration (not recommended for SOLiD data) using GATK or a similar tool.
• Indel local realignment using GATK or SMRA.

Usage

Atlas-SNP2 usage [Atlas-SNP]
Atlas-Indel2 usage [Atlas-Indel]
VcfPrinter usage [VcfPrinter]
Best practices and Workflows [Best Practices and Workflows]

Output

The output of Atlas2 is a simple VCF file. The sample column includes the estimated genotype (GT), the number of major variant reads (VR), the number of reference reads (RR) and the total read depth (DP) at that site. There are also two fields for the genotype quality (GQ) and a genotype filter (FT); these fields may be left blank but may be used for post processing and in future versions of Atlas.

Atlas2 Cloud

We are actively working on making our services more accessible to our end users and to that end we developed Atlas2 Cloud. Please refer to our BMC Genomics article Atlas2 Cloud: a framework for personal genome analysis in the cloud for more information.

Changelog

• Version 1.4.3 released on 3 January,2013. New options in Atlas-SNP2, major bug fixes in Atlas-INDEL2 and major updates to vcfPrinter.
• Version 1.4.1 adds new output options for Atlas-SNP2
• Version 1.4.1 adds new options for Atlas-Indel2, and makes several bugfixes
  Full changelog: [Changelog]

Acknowledgements

A special thanks to the users/developers listed below for their contributions to the Atlas2 project.
- Bradford Powell

Contact

Dr. Fuli Yu (fyu@bcm.edu)
Danny Challis (challis@bcm.edu)
Jin Yu (jy2@bcm.edu)

Human Genome Sequencing Center (HGSC)
Baylor College of Medicine (BCM)
Houston, TX, USA