cutesv

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

usage

nexus run --nf-workflow variant_calling_cutesv.nf \
    -c nextflow.config \
    -w work/ \
    --samples_tsv_file samples.tsv \
    --output_dir results/ \
    --reference_genome_fasta_file /path/to/file.fasta \
    --params_cutesv "--max_cluster_bias_INS 1000 --diff_ratio_merging_INS 0.9 --max_cluster_bias_DEL 1000 --diff_ratio_merging_DEL 0.5 --min_support 3 --min_mapq 20 --min_size 30 --max_size -1 --report_readid --genotype"

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.
--params_cutesv	CuteSV parameters (default: ‘“–max_cluster_bias_INS 1000 –diff_ratio_merging_INS 0.9 –max_cluster_bias_DEL 1000 –diff_ratio_merging_DEL 0.5 –min_support 3 –min_mapq 20 –min_size 30 –max_size -1 –report_readid –genotype”’). Note that the parameters need to be wrapped in quotes.