Abstract base class for tasks that involve running the GATK.
Genotypes one or more GVCFs concurrently.
Runs the GATK haplotype caller i GVCF mode on a single sample.
Runs the BAM transforming IndelRealigner step.
Runs Mutect 1 from the separate Mutect/CGA tools distribution
Task for running MuTect2 from the GATK 3.5+ distribution.
Runs the realigner target creator step of the process.
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.
Runs the GATK walker that splits reads at N operators in cigars so that RNA-seq BAMs can be fed into the HaplotypeCaller