pbfusion

Identify RNA variants in long-read RNA sequencing BAM files using Pbfusion

usage

nexus run --nf-workflow variant_calling_pbfusion.nf \
    -c nextflow.config \
    -w work/ \
    --samples_tsv_file samples.tsv \
    --output_dir results/ \
    --reference_genome_fasta_file /path/to/file.fasta \
    --reference_genes_gtf_file /path/to/file.gtf \
    --params_pbfusion_discover "--min-coverage 3 --min-mean-mapq 20 --gtf-transcript-allow-lncRNA"

Note

Nextflow config files are available here. Use the config file that matches your installed nexus version (e.g. nexus_v0.2.0_nextflow_slurm.config).

parameters

parameter	description
--samples_tsv_file	TSV file with the following columns: ‘sample_id’, ‘bam_file’, ‘bam_bai_file’.
--output_dir	Directory to which output files will be copied.
--reference_genome_fasta_file	Reference genome FASTA file.
--reference_genes_gtf_file	Reference genes GTF file.
--params_pbfusion_discover	Pbfusion discover parameters (default: ‘“–min-coverage 3 –min-mean-mapq 20 –gtf-transcript-allow-lncRNA”’). Note that the parameters need to be wrapped in quotes.