BioGraph Command Reference - spiralgenetics/biograph GitHub Wiki

See Customizing the BioGraph Pipeline for an overview of the essential BioGraph commands.

Most BioGraph work is performed with a few essential commands. For more details on these commands, consult the following pages:

• reference: convert a FASTA to the BioGraph reference format
• full_pipeline: produce variant calls from reads
• create: convert reads to the BioGraph format
• discovery: call putative variants versus a reference
• coverage: genotype variants
• grm: truvari anno grm
• qual_classifier: assign a quality score to variants and filter on a threshold

Additional Commands

• stats: compute BioGraph QC statistics
• refhash: uniquely identify the genetic reference used for a VCF, FASTA, SAM/BAM, or BioGraph reference directory
• vdb Variant DataBase BETA: the BioGraph variant database