GATK

note

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

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

DOI: 10.1101/201178, 10.1002/0471250953.bi1110s43, 10.1038/ng.806, 10.1101/gr.107524.110

Apache License 2.0

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
- contents: '#:SENTIEON_QCAL_TABLE:Arguments:Recalibration'
  num_lines: 3
gatk/varianteval:
  contents: '#:GATKTable:TiTvVariantEvaluator'