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GATK

Wide variety of tools with a primary focus on variant discovery and genotyping

https://www.broadinstitute.org/gatk/

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/analyze_saturation_mutagenesis:
  contents: ">>Reads in disjoint pairs evaluated separately:"
  fn: "*.readCounts"
  num_lines: 10
gatk/base_recalibrator:
  contents: "#:GATKTable:Arguments:Recalibration"
  num_lines: 3
gatk/varianteval:
  contents: "#:GATKTable:TiTvVariantEvaluator"