Variant Discovery in High-Throughput Sequencing Data
Developed by the Data Science and Data Engineering group at the Broad Institute, the GATK toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
AnalyzeSaturationMutagenesis is a (beta!) tool for counting variants in saturation mutagenesis experiments. It accepts mapped reads and a reference sequence and outputs a number of files for further analysis.
BaseRecalibrator is a tool for detecting systematic errors in read base quality scores of aligned high-throughput sequencing reads. It outputs a base quality score recalibration table that can be used in conjunction with the PrintReads tool to recalibrate base quality scores.
VariantEval is a general-purpose tool for variant evaluation. It gives information about percentage of variants in dbSNP, genotype concordance, Ti/Tv ratios and a lot more.
File search patterns
gatk/varianteval: contents: "#:GATKTable:TiTvVariantEvaluator" shared: true gatk/base_recalibrator: contents: "#:GATKTable:Arguments:Recalibration" num_lines: 3 gatk/analyze_saturation_mutagenesis: fn: "*.readCounts" contents: ">>Reads in disjoint pairs evaluated separately:" num_lines: 10