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 GenotypeGvcfs extends GatkTask

   

   Genotypes one or more GVCFs concurrently.

3. class HaplotypeCaller extends GatkTask

   

   Runs the GATK haplotype caller in 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 SplitIntervalsForCallingRegions extends SimpleInJvmTask with Partitioner[PathToIntervals]

   

   Creates a set of interval list files given a sequence dictionary.

   Creates a set of interval list files given a sequence dictionary.

   If no intervals are given, it will create one or more interval list files per reference sequence.

   Each input interval will be broken up into non-overlapping regions of at most maxBasesPerScatter size. Each output interval list will cover at most maxBasesPerScatter non-overlapping bases.

10. 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