ArrayIndexOutOfBoundsException error in BaseRecalibratorSpark
Creating a list of common SNPs for use with GetBayesianHetCoverage
Description and examples of the steps in the ACNV case workflow
Description and examples of the steps in the CNV case and CNV PoN creation workflows
GATK CNV Toolchain in Firehose and FAQ Broad Internal
GATK4 ApplyBQSRSpark VS PrintReadsSpark
GATK4Alpha MarkDuplicates crashing
How does the BwaSpark in GATK4 control the number of threads
How to Call somatic copy number variants using GATK4 CNV
How to Run FlagStatSpark on a cloud Spark cluster
How to Run the GATK4 Docker locally and take a look inside
HOWTO Run GATK CNV and GATK ACNV using premade Queue scripts Broad Internal
Howto Run GATK4 in a Docker container
No plots produced by AnalyzeCovariates GATK4Alpha
Overview of GetBayesianHetCoverage for heterozygous SNP calling
Using GenomicsDBImport to consolidate GVCFs for input to GenotypeGVCFs in GATK4
WDL for GATK CNV and GATK ACNV
Which dotkits should you load to run GATK CNV or ACNV Broad Internal
Why is java using 1000 of my CPU when running a singlethreaded tool in gatkprotectedjar