svisionpro

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

usage

nexus run --nf-workflow variant_calling_svisionpro.nf \
    -c nextflow.config \
    -w work/ \
    --samples_tsv_file samples.tsv \
    --output_dir results/ \
    --reference_genome_fasta_file /path/to/file.fasta \
    --svisionpro_model_file /path/to/file \
    --params_svisionpro "--detect_mode somatic --preset hifi --min_supp 3 --min_mapq 20 --min_sv_size 30 --max_sv_size 1000000 --device cpu --img_size 256" \
    --params_svisionpro_extract "--extract somatic --min_supp 3"

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’.
--output_dir	Directory to which output files will be copied.
--reference_genome_fasta_file	Reference genome FASTA file.
--svisionpro_model_file	SVision-pro model file.
--params_svisionpro	SVision-pro parameters (default: ‘“–detect_mode somatic –preset hifi –min_supp 3 –min_mapq 20 –min_sv_size 30 –max_sv_size 1000000 –device cpu –img_size 256”’). Note that the parameters need to be wrapped in quotes.
--params_svisionpro_extract	SVision-pro extract_op.py parameters (default: ‘“–extract somatic –min_supp 3”’). Note that the parameters need to be wrapped in quotes.