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Variant recalibration software tools | Whole-genome sequencing data analysis

Accurate genomic variant detection is an essential step in gleaning medically useful information from genome data. However, low concordance among variant-calling methods reduces confidence in the clinical validity of whole genome and exome sequence…
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GATK-Queue
Desktop

GATK-Queue Genome Analysis Toolkit-Queue

A command-line scripting framework for defining multi-stage genomic analysis…

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…

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GATK
Desktop

GATK Genome Analysis ToolKit

Focuses on variant discovery and genotyping. GATK provides a toolkit, developed…

Focuses on variant discovery and genotyping. GATK provides a toolkit, developed at the Broad Institute, composed of several tools and ables to support projects of any size. The application compiles…

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GATK…
Desktop

GATK VariantRecalibrator

Builds a recalibration model to score variant quality for filtering purposes.…

Builds a recalibration model to score variant quality for filtering purposes. VariantRecalibrator performs the first pass in a two-stage process called VQSR; the second pass is performed by the…

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RG
Desktop

RG ReliableGenome

Calculates concordant and discordant regions with respect to a set of surveyed…

Calculates concordant and discordant regions with respect to a set of surveyed variant calling (VC) pipelines. ReliableGenome combines call sets derived by multiple pipelines from arbitrary numbers…

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BAYSIC
Desktop

BAYSIC BAYeSian Integrated Caller

Provides a method for combining sets of SNP variant calls produced by different…

Provides a method for combining sets of SNP variant calls produced by different variant calling programs. The integrated set of SNP variant calls produced by BAYSIC™ improves the sensitivity and…

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FMFilter
Desktop

FMFilter

Filters candidate variants according to the given criteria. FMFilter can handle…

Filters candidate variants according to the given criteria. FMFilter can handle compound heterozygous and de novo models properly. It offers options to make filtering according to genotype quality,…

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VariantMetaCall…
Desktop

VariantMetaCaller

Automatically integrates variant calling pipelines into a better performing…

Automatically integrates variant calling pipelines into a better performing overall model that also predicts accurate variant probabilities. VariantMetaCaller uses Support Vector Machines to combine…

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