Commands

Alphabetical reference for every Exacto command line interface. For end-to-end walkthroughs that compose these into pipelines, see Pipelines.

Available Commands

Command	Description
annotate-vars	Annotate variants.
build-genome-var-graph	Build a genome variation graph.
build-transcriptome-var-graph	Build a transcriptome variation graph.
call-germline-dna-vars	Call germline DNA variants in a long-read DNA BAM file.
call-peptide-vars	Call peptide variants by comparing translated mutant proteoforms to a reference proteome.
call-rna-vars	Call RNA variants in a long-read RNA assembly BAM file.
call-somatic-dna-vars	Call somatic DNA variants in tumor and matched normal long-read DNA BAM files.
integrate-vars	Integrate DNA and RNA variants.
remove-unspliced-rnas	Remove unspliced RNAs.
translate-seqs	Translate transcript sequences in a FASTA or FASTQ file to peptide sequences.
translate-structs	Translate transcript structures to primary structures.