GATK
For gatk, the following wrappers are available:
- GATK APPLYBQSR
- GATK APPLYBQSRSPARK
- GATK APPLYVQSR
- GATK BASERECALIBRATOR
- GATK BASERECALIBRATORSPARK
- GATK CALCULATECONTAMINATION
- GATK CALLCOPYRATIONSEGMENTS
- GATK CLEANSAM
- GATK COLLECTALLELICCOUNTS
- GATK COLLECTREADCOUNTS
- GATK COMBINEGVCFS
- GATK DENOISEREADCOUNTS
- GATK DEPTHOFCOVERAGE
- GATK ESTIMATELIBRARYCOMPLEXITY
- GATK FILTERMUTECTCALLS
- GATK GENOMICSDBIMPORT
- GATK GENOTYPEGVCFS
- GATK GETPILEUPSUMMARIES
- GATK HAPLOTYPECALLER
- GATK INTERVALLISTTOBED
- GATK LEARNREADORIENTATIONMODEL
- GATK LEFTALIGNANDTRIMVARIANTS
- GATK MARKDUPLICATESSPARK
- GATK MODELSEGMENTS
- GATK MUTECT2
- GATK PRINTREADSSPARK
- GATK SCATTERINTERVALSBYNS
- GATK SELECTVARIANTS
- GATK SPLITINTERVALS
- GATK SPLITNCIGARREADS
- GATK VARIANTANNOTATOR
- GATK VARIANTEVAL
- GATK VARIANTFILTRATION
- GATK VARIANTRECALIBRATOR
- GATK VARIANTSTOTABLE