The following standalone tools can be used with the NVIDIA Clara Parabricks Pipelines software. Click on a tool name for tool-specific options.
Tool |
Details |
Apply BQSR report to a BAM file and generate new BAM file |
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Convert a BAM file to FASTQ |
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Collect WGS Metrics on a BAM file |
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Sort a BAM file |
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Collect BQSR report on a BAM file |
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Collect multiple classes of metrics on a BAM file |
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Annotate variants based on a dbSNP |
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Run GPU-DeepVariant for calling germline variants |
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Run bwa mem, coordinate sorting, marking duplicates, and Base Quality Score Recalibration |
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Convert a GVCF to VCF |
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Run GPU-HaplotypeCaller for calling germline variants |
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Index a GVCF file |
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Run GPU-Mutect2 for tumor-normal analysis |
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Generate the final VCF output of doing mutect PON |
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Build an index for a PON file, which is the prerequisite to performing mutect PON |
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Run RNA-seq data through the fq2bam pipeline |
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Identify candidate fusion transcripts supported by Illumina reads |