Detailed Tutorials for Parabricks Pipelines

These 'How-To' sections go into more detail on how to use the NVIDIA Parabricks software using larger data sets, a wider variety of options and different ways of analyzing the data.

We start with how to perform germline and somatic calling. Additional discussions on somatic, exome, and transcriptome calling will be available in the future.

• WGS Variant Calling
  
  • Software Requirements
  • Hardware Requirements
  • Introduction
  • Example data
  • Downloading and Indexing a Reference Genome and Known Sites
  • Aligning Reads
  • Generating a Comprehensive Set of Variant Calls with DeepVariant and HaplotypeCaller
• WGS Somatic Small Variant Calling
  
  • Software Prerequisites
  • Compute Requirements and Configuration
  • Introduction
  • Download Example FASTQ Files
  • Downloading and Indexing a Reference Genome and Known Sites
  • Index Reference Genome
  • Step1: Aligning the Fastq Files to the Reference Genome
  • Step2: Generating a Set of Small Variant Calls Using Parabricks Mutect2
  • Step3: For Validating the SNV and MNV Variants with truth set
  • Use GATK4 FilterMutectCalls to Apply Filters to the Raw Output of Mutect2
  • References and Useful Links