GATK3 Haplotype Caller (Public)

Run GATK3 Best Practices pipeline on paired end reads and perform variant calls using both Haplotype Caller and Unified Genotyper. To run this pipeline, click on Run a pipeline and select “Demo GATK3 Haplotype Caller Pipeline” from the GATK3 Haplotype Caller Project. Feel free to use "PGP HU34D5B9 “FASTQ” exome" as the input data set, which is 2 sets of paired end fastq files.