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Genome Analysis Toolkit-Queue GATK-Queue

A command-line scripting framework for defining multi-stage genomic analysis pipelines combined with an execution manager that runs those pipelines from end-to-end. Often processing genome data includes several steps to produces outputs, for example our BAM to VCF calling pipeline include among other things: local realignment around indels; emitting raw SNP calls; emitting indels, masking the SNPs at indels; annotating SNPs using chip data; labeling suspicious calls based on filters; creating a summary report with statistics. Running these tools one by one in series may often take weeks for processing, or would require custom scripting to try and optimize using parallel resources. With a Queue script users can semantically define the multiple steps of the pipeline and then hand off the logistics of running the pipeline to completion. Queue runs independent jobs in parallel, handles transient errors, and uses various techniques such as running multiple copies of the same program on different portions of the genome to produce outputs faster.

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GATK-Queue classification

GATK-Queue specifications

Software type:
Framework/Library
Restrictions to use:
None
Parallelization:
MapReduce
Version:
3.4-46
High performance computing:
Yes
Interface:
Command line interface
Operating system:
Unix/Linux
Computer skills:
Advanced
Stability:
Stable
Maintained:
Yes

GATK-Queue distribution

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No versioning.

Credits

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Publications

Institution(s)

Program in Medical and Population Genetics, The Broad Institute of Harvard and MIT, Cambridge, MA, USA

Link to literature

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