build-genome-var-graph

Build a genome variation graph.

Usage

Template:

exacto build-genome-var-graph \
    --variants-tsv-file <variants_tsv_file> \
    --fasta-file <fasta_file> \
    --output-fasta-file <output_fasta_file> \
    --sequence-prefix <sequence_prefix> \
    [--remove-unknown-bases REMOVE_UNKNOWN_BASES] \
    [--only-variant-sequences ONLY_VARIANT_SEQUENCES] \
    [--graph-type GRAPH_TYPE] \
    [--num-threads NUM_THREADS]

Example:

exacto build-genome-var-graph \
    --variants-tsv-file tumor_dna_rna_variants_integrated.tsv \
    --fasta-file reference_genome.fasta \
    --output-dir genome_var_graph_outputs/

Description

Build a genome variation graph.

At a glance

Inputs: *.tsv (variants), *.fasta (reference genome)

Outputs: Graph files written to --output-dir

Typical next step: Endpoint — feeds downstream graph-aware analyses

Required arguments

Flag	Type	Description
`--variants-tsv-file`	`str`	Variants TSV file. Expected columns: ‘variant_id’, ‘chromosome_1’, ‘position_1’, ‘operation_1’, ‘strand_1’, ‘chromosome_2’, ‘position_2’, ‘operation_2’, ‘strand_2’, ‘sequence’.
`--fasta-file`	`str`	Reference genome FASTA file (variation graph backbone).
`--output-fasta-file`	`str`	Output FASTA file.
`--sequence-prefix`	`str`	Sequence prefix.

Optional arguments

Flag	Type	Default	Description
`--remove-unknown-bases`	`str2bool`	`yes`	If ‘yes’, then unknown nucleotides (‘N’ or ‘n’) are removed.
`--only-variant-sequences`	`str2bool`	`no`	If ‘yes’, then only variant sequences will be output.
`--graph-type`	`str`	`individual`	Variation graph type. Either ‘individual’ or ‘population’.
`--num-threads`	`int`	`4`	Number of threads.