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v4.0.1
  • What's New?
    • Licensing Changes
    • Supported Tools
    • WDL/Nextflow Workflows
    • Improvements
    • Bug Fixes
  • Getting Started with Clara Parabricks
    • Installation Requirements
      • Hardware Requirements
      • Software Requirements
      • Verifying Hardware and Software Requirements
        • Checking available NVIDIA hardware and driver
        • Checking available CPU RAM and threads
        • Checking nvidia-docker2 installation
        • Checking python version
    • Getting the Software
    • Running Clara Parabricks
      • From the Command Line
      • Using an AWS AMI
    • Performance Tuning
      • Use a Fast SSD
        • DGX Users
      • Specifying which GPUs to use
    • Uninstalling the software
  • Software Overview
    • Software Tools
    • Clara Parabricks WDL/Nextflow Workflows
    • Compatible CPU Software Versions
  • Tutorials
    • Getting The Sample Data
    • FQ2BAM Tutorial
    • HaplotypeCaller Tutorial
  • How-Tos
    • Whole-Genome Small 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, HaplotypeCaller, and Strelka
      • Annotating Variant Calls with Information from Databases
    • Whole-Genome 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 Clara 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
      • Annotating Variant Calls with Information from Databases
      • References and Useful Links
  • Tool Reference
    • Tools By Category
    • Tools Alphabetically By Name
  • Help
    • Frequently asked questions
    • User Forum
  • References
    • Publications
      • Academic References to Clara Parabricks
      • See Also
    • Third Party Software Notices
      • ABSEIL
      • BWA
      • DEEPVARIANT
      • GATK
      • HTSLIB
      • ISA-L
      • NUCLEUS
      • SAMTOOLS
      • STAR
      • STAR-FUSION
      • TCMALLOC
      • TENSORFLOW
    • Comparison with Baseline Tools
      • Comparing BAM Files
      • Comparing BQSR Reports
      • Comparing VCF Files
Clara Parabricks
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  • References

ReferencesΒΆ

  • Publications
  • Third Party Software Notices
  • Comparison with Baseline Tools
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