integrate-vars

Integrate DNA and RNA variants.

Usage

Template:

exacto integrate-vars \
    --annotated-dna-vars-tsv-file <annotated_dna_vars_tsv_file> \
    --rna-vars-tsv-file <rna_vars_tsv_file> \
    --reference-gene-annotation-file <reference_gene_annotation_file> \
    --reference-gene-annotation-source <reference_gene_annotation_source> \
    --reference-gene-annotation-assembly <reference_gene_annotation_assembly> \
    --reference-gene-annotation-version <reference_gene_annotation_version> \
    --output-tsv-file <output_tsv_file> \
    [--num-threads NUM_THREADS] \
    [--max-exon-offset MAX_EXON_OFFSET] \
    [--max-transcript-boundary-offset MAX_TRANSCRIPT_BOUNDARY_OFFSET] \
    [--max-intergenic-distance MAX_INTERGENIC_DISTANCE]

Example:

exacto integrate-vars \
    --annotated-dna-vars-tsv-file tumor_specific_dna_variants.annotated.tsv \
    --rna-vars-tsv-file rna_variants_outputs/tumor_exacto_rna_variant_calls.tsv \
    --reference-gene-annotation-file gencode.gtf.gz \
    --reference-gene-annotation-source gencode \
    --reference-gene-annotation-assembly hg38 \
    --reference-gene-annotation-version v44 \
    --output-tsv-file tumor_dna_rna_variants_integrated.tsv

Description

Integrate DNA and RNA variants.

At a glance

Inputs: *.tsv (annotated DNA variants), *.tsv (RNA variants), *.gtf.gz

Outputs: *.tsv (integrated DNA + RNA variants)

Typical next step: translate-structs

Required arguments

Flag	Type	Description
`--annotated-dna-vars-tsv-file`	`str`	Annotated DNA variant callset TSV file.
`--rna-vars-tsv-file`	`str`	RNA variant callset TSV file.
`--reference-gene-annotation-file`	`str`	Reference gene annotation file.
`--reference-gene-annotation-source`	`str`	Reference gene annotation source.
`--reference-gene-annotation-assembly`	`str`	Reference gene annotation assembly (e.g. ‘hg38’).
`--reference-gene-annotation-version`	`str`	Reference gene annotation version (e.g. ‘v41’).
`--output-tsv-file`	`str`	Output TSV file.

Optional arguments

Flag	Type	Default	Description
`--num-threads`	`int`	`4`	Number of threads.
`--max-exon-offset`	`int`	`2`	Maximum exon offset.
`--max-transcript-boundary-offset`	`int`	`10000`	Maximum transcript boundary offset.
`--max-intergenic-distance`	`int`	`100000`	Maximum intergenic distance.