call-rna-vars

Call RNA variants in a long-read RNA-seq BAM file.

Usage

Template:

exacto call-rna-vars \
    --bam-file <bam_file> \
    --bam-bai-file <bam_bai_file> \
    --reference-genome-fasta-file <reference_genome_fasta_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-dir <output_dir> \
    --output-prefix <output_prefix> \
    [--num-threads NUM_THREADS] \
    [--chunk-size CHUNK_SIZE] \
    [--min-mapping-quality MIN_MAPPING_QUALITY] \
    [--reference-transcript-scoring-method REFERENCE_TRANSCRIPT_SCORING_METHOD] \
    [--reference-transcript-selection-strategy REFERENCE_TRANSCRIPT_SELECTION_STRATEGY] \
    [--reference-transcript-top-k REFERENCE_TRANSCRIPT_TOP_K] \
    [--reference-transcript-threshold REFERENCE_TRANSCRIPT_THRESHOLD] \
    [--min-average-base-quality MIN_AVERAGE_BASE_QUALITY] \
    [--temp-dir TEMP_DIR]

Example:

exacto call-rna-vars \
    --bam-file tumor_transcriptome_assembly.sorted.filtered.bam \
    --bam-bai-file tumor_transcriptome_assembly.sorted.filtered.bam.bai \
    --reference-genome-fasta-file reference_genome.fasta \
    --reference-gene-annotation-file gencode.gtf.gz \
    --reference-gene-annotation-source gencode \
    --reference-gene-annotation-assembly hg38 \
    --reference-gene-annotation-version v44 \
    --output-dir rna_variants_outputs/ \
    --output-prefix tumor

Description

Call RNA variants in a long-read RNA-seq BAM file.

NoteAt a glance

Inputs: *.bam, *.bam.bai, *.fasta, *.gtf.gz

Outputs: *.tsv (RNA variants), *.tsv (transcript structures) under --output-dir

Typical next step: integrate-vars, translate-structs

Required arguments

Flag	Type	Description
--bam-file	str	Input BAM file.
--bam-bai-file	str	Input BAM.BAI file.
--reference-genome-fasta-file	str	Reference genome FASTA 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-dir	str	Output directory.
--output-prefix	str	Output prefix.

Optional arguments

Flag	Type	Default	Description
--num-threads	int	4	Number of threads.
--chunk-size	int	10000	Chunk size for variant calling.
--min-mapping-quality	int	20	Minimum mapping quality.
--reference-transcript-scoring-method	str	cosine_similarity	Reference transcript scoring method.
--reference-transcript-selection-strategy	str	top_k	Reference transcript scoring method.
--reference-transcript-top-k	int	1	Select top k reference transcripts.
--reference-transcript-threshold	float	0.9	Select reference transcripts with scores greater than or equal to the threshold.
--min-average-base-quality	float	30	Minimum average base quality.
--temp-dir	str		Temp directory.