Pipeline Tools Overview

Tool

Details

deepvariant_germline

Run the germline pipeline from FASTQ to VCF using a deep neural network analysis

denovomutation

(BETA) Run the de novo mutation pipeline with three samples for de novo variant detection

germline

Run the germline pipeline from FASTQ to VCF

human_par

Run the germline pipeline from FASTQ to VCF with correct ploidy values for human sex chromosome handling

rna_gatk

Run the GATK Best Practices pipeline for RNA-seq data from FASTQ to VCF

somatic

Run the somatic pipeline from FASTQ to VCF

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