GATK4 germline short variant discovery (SNPs + Indels)ΒΆ

An HPC workflow for running the HaplotypeCaller from GATK4 in GVCF mode according to GATK Best Practices. check out these GATK documents for more details:

  • https://github.com/gatk-workflows/broad-prod-wgs-germline-snps-indels/blob/1.1.1/JointGenotypingWf.wdl

  • https://github.com/broadinstitute/warp/blob/master/tasks/broad/JointGenotypingTasks.wdl

  • https://github.com/broadinstitute/warp/blob/master/pipelines/broad/dna_seq/germline/joint_genotyping/JointGenotyping.wdl