gatk

Type Members

1. abstract class GatkTask extends ProcessTask with JarTask with FixedResources with Configuration

   

   Abstract base class for tasks that involve running the GATK.

2. class GenotypeSingleGvcf extends GatkTask

   

   Genotypes a single GVCF.

3. class HaplotypeCaller extends GatkTask

   

   Runs the GATK haplotype caller i GVCF mode on a single sample.

4. class IndelRealigner extends GatkTask

   

   Runs the BAM transforming IndelRealigner step.

5. class IndelRealignment extends Pipeline

   

   Annotations

   @ClpAnnotation()

6. class Mutect1 extends GatkTask

   

   Runs Mutect 1 from the separate Mutect/CGA tools distribution

7. class Mutect2 extends GatkTask with FixedResources

   

   Task for running MuTect2 from the GATK 3.5+ distribution.

8. class RealignerTargetCreator extends GatkTask

   

   Runs the realigner target creator step of the process.

9. class SplitNCigarReads extends GatkTask

   

   Runs the GATK walker that splits reads at N operators in cigars so that RNA-seq BAMs can be fed into the HaplotypeCaller