colorsv

Identify somatic structural variants in long-read DNA sequencing GFA files using colorSV

usage

nexus run --nf-workflow variant_calling_colorsv.nf \
    -c nextflow.config \
    -w work/ \
    --samples_tsv_file samples.tsv \
    --output_dir results/ \
    --reference_genome_fasta_file /path/to/file.fasta \
    --filter_bed_file /path/to/file.bed \
    --params_colorsv_preprocess "--read-sep /" \
    --params_colorsv_call ""

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’, ‘gfa_file’, ‘tumor_ids’.
--output_dir	Directory to which output files will be copied.
--reference_genome_fasta_file	Reference genome FASTA file.
--filter_bed_file	BED file of regions to exclude.
--params_colorsv_preprocess	colorSV preprocess parameters (default: ‘“–read-sep /”’). Note that the parameters need to be wrapped in quotes.
--params_colorsv_call	colorSV call parameters (default: ‘““’). Note that the parameters need to be wrapped in quotes.