Clara Parabricks Pipelines

Getting Started

• NVIDIA CLARA PARABRICKS PIPELINES
  • What is CLARA PARABRICKS Pipelines?
  • Why use CLARA PARABRICKS Pipelines?
  • SOFTWARE OVERVIEW
  • SOFTWARE TOOLS OVERVIEW
  • PIPELINES OVERVIEW
• GETTING STARTED
  • QUICKSTART GUIDE
  • PERFORMANCE TUNING
  • RUNNING NVIDIA CLARA PARABRICKS PIPELINES
  • OUTPUT COMPARISON
• LOCAL INSTALLATION
  • PREREQUISITES
  • INSTALLATION STEPS
  • INSTALLATION OPTIONS
  • INSTALLING WITH SINGULARITY 3.0 OR HIGHER
  • UNINSTALLING PARABRICKS

Standalone Tools

• FASTQ AND BAM PROCESSING OVERVIEW
  • FQ2BAM
  • BQSR
  • APPLYBQSR
• VARIANT CALLERS
  • BCFTOOLS CALL
  • HAPLOTYPECALLER
  • MUTECTCALLER
  • VARSCAN
  • VARSCAN WORKFLOW
  • SOMATICSNIPER
  • SOMATICSNIPER WORKFLOW
  • DEEPVARIANT
  • CNVKIT
  • MANTA
  • STRELKA
  • STRELKA WORKFLOW
• RNA
  • RNA FQ2BAM
  • STAR-FUSION
• QUALITY CONTROL AND BAM PROCESSING
  • SPLITNCIGAR
  • SAMTOOLS MPILEUP
  • BCFTOOLS MPILEUP
  • BAMMETRICS
  • COLLECTMULTIPLEMETRICS
• VARIANT PROCESSING
  • DBSNP
  • MUTATION SIGNATURE
  • CNNSCOREVARIANTS
  • VARIANTFILTRATION
  • VQSR
• JOINT CALLING
  • TRIO COMBINE VGCF
  • GLNEXUS
• GVCF PROCESSING
  • INDEX GVCF
  • GENOTYPEGVCF

Pipelines

• GERMLINE PIPELINE
  • QUICK START
  • DNAnexus
  • COMPATIBLE CPU BASED BWA-MEM, GATK4 COMMANDS
  • OPTIONS
  • DNANEXUS
• DEEPVARIANT GERMLINE PIPELINE
  • QUICK START
  • OPTIONS
• HUMAN_PAR PIPELINE
  • QUICK START
  • COMPATIBLE CPU BASED BWA-MEM, GATK4 COMMANDS
  • OPTIONS
• SOMATIC PIPELINE
  • QUICK START
  • OPTIONS
• RNA PIPELINE
  • QUICK START
  • OPTIONS

FAQs and Troubleshooting

• FAQS AND TROUBLESHOOTING
  • CLI USAGE