Atlas Suite
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Application data |
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| Created by | Fuli Yu, Danny Challis, Jin Yu, Uday Evani |
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| Biological application domain(s) | SNP detection, Indel detection |
| Principal bioinformatics method(s) | Variant calling |
| Technology | Illumina, 454, ABI SOLiD |
| Created at | Human Genome Sequencing Center (HGSC) at Baylor College of Medicine. |
| Maintained? | Yes |
| Input format(s) | SAM, BAM |
| Output format(s) | VCF |
| Programming language(s) | Ruby, C |
| Licence | BSD |
| Operating system(s) | POSIX |
Summary: Atlas 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. SNPs may be called using the Atlas-SNP2 application and indels may be called using the Atlas-Indel2 application.
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Description
Atlas 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. 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.
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