integrate-vars

Integrate DNA and RNA variants.

Usage

Template:

exacto integrate-vars \
    --dna-variants-tsv-file <dna_variants_tsv_file> \
    --rna-variants-tsv-file <rna_variants_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 \
    --dna-variants-tsv-file tumor_somatic_dna_variants.tsv \
    --rna-variants-tsv-file rna_variants/tumor_exacto_assembled_transcript_variants.tsv \
    --reference-gene-annotation-file gencode.gtf.gz \
    --reference-gene-annotation-source gencode \
    --reference-gene-annotation-assembly hg38 \
    --reference-gene-annotation-version v45 \
    --output-tsv-file tumor_integrated_variants.tsv

Description

Integrate DNA and RNA variants.

At a glance

Inputs: *.tsv (DNA variants from call-somatic-dna-vars, or any callset in the variant grammar), *_exacto_assembled_transcript_variants.tsv (from call-rna-transcript-vars), *.gtf.gz

Outputs: *.tsv (RNA variants linked to the DNA variants that explain them)

Typical next step: translate-transcripts

Required arguments

Flag	Type	Description
`--dna-variants-tsv-file`	`str`	DNA variant callset TSV file. Accepts either the full exacto somatic-variants schema (from call-somatic-dna-vars) or a bare-bones variant grammar with just the columns: origin, variant_id, chromosome_1, position_1, strand_1, operation_1, chromosome_2, position_2, strand_2, operation_2, sequence. Columns are matched by header name; any omitted trailing columns default to empty/0.
`--rna-variants-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 difference in exon number between an RNA and a DNA position in or near one listed reference transcript.
`--max-transcript-boundary-offset`	`int`	`10000`	Maximum distance outside a reference transcript end at which a position counts as in the exon at that end.
`--max-intergenic-distance`	`int`	`100000`	Maximum distance between an RNA and a DNA position that both lie outside every listed reference transcript.