severus

Identify somatic structural variants in long-read DNA sequencing BAM files using Severus

usage

nexus run --nf-workflow variant_calling_severus.nf \
    -c nextflow.config \
    -w work/ \
    --samples_tsv_file samples.tsv \
    --output_dir results/ \
    --vntr_bed_file /path/to/file.bed \
    --params_severus "--min-support 3 --min-sv-size 30 --min-mapq 20 --output-read-ids --bp-cluster-size 50"

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’, ‘tumor_bam_file’, ‘tumor_bam_bai_file’, ‘normal_bam_file’, ‘normal_bam_bai_file’, ‘phased_vcf_file’.
--output_dir	Directory to which output files will be copied.
--vntr_bed_file	Tandem repeat regions BED file.
--params_severus	Severus parameters (default: ‘“–min-support 3 –min-sv-size 30 –min-mapq 20 –output-read-ids –bp-cluster-size 50”’). Note that the parameters need to be wrapped in quotes.