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GATK / Genome Analysis ToolKit
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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 an assortment of command line allowing one to analyze of high-throughput sequencing (HTS) data in various formats such as SAM, BAM, CRAM or VCF. The website includes multiple documentation for guiding users.
RG / ReliableGenome
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 of datasets and interpolates expected concordance for genomic regions without data. Our method can be applied to arbitrary VC pipelines and the resulting genomic partitions can be used for variant filtering, annotation and prioritization or for focusing computational resources on hard-to-analyse regions of the genome.
Automatically integrates variant calling pipelines into a better performing overall model that also predicts accurate variant probabilities. VariantMetaCaller uses Support Vector Machines to combine multiple information sources generated by variant calling pipelines and estimates probabilities of variants. This novel method had significantly higher sensitivity and precision than the individual variant callers in all target region sizes, ranging from a few hundred kilobases to whole exomes. We also demonstrated that VariantMetaCaller supports a quantitative, precision based filtering of variants under wider conditions. Specifically, the computed probabilities of the variants can be used to order the variants, and for a given threshold, probabilities can be used to estimate precision. Precision then can be directly translated to the number of true called variants, or equivalently, to the number of false calls, which allows finding problem-specific balance between sensitivity and precision.
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