GATK - Genome Analysis Toolkit | Tool name | GATK - Genome Analysis Toolkit |
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| URL | http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit |
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| Important features | 1. The Genome Analysis Toolkit (GATK) is a software package which can perform various NGS analysis.
2. It solves the data management challenge by separating data access patterns from analysis algorithms, using the functional programming philosophy of Map/Reduce. |
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| Citations | McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010 Sep;20(9):1297-303. Epub 2010 Jul 19. PubMed PMID: 20644199; PubMed
Central PMCID: PMC2928508. |
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| Year of publication | 2010 |
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| Rank by usage frequency | 100 |
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| Comments | |
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| Function | Realignment, SNP discovery, Indel discovery |
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| Category | Free, Downloadable |
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| License | |
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| Status | |
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| Input file format | SAM,BAM, FASTA |
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| Output file format | VCF |
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| Operating system | Linux |
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| Operating language | Java, Python |
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| Platform | ABI SOLiD, Illumina/Solexa, Roche 454 |
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