GATK

Description

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.

Supported tools:

• AnalyzeSaturationMutagenesis
• BaseRecalibrator
• VariantEval

AnalyzeSaturationMutagenesis

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

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

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"
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