nanomonsv

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

usage

nexus run --nf-workflow variant_calling_nanomonsv.nf \
    -c nextflow.config \
    -w work/ \
    --samples_tsv_file samples.tsv \
    --output_dir results/ \
    --reference_genome_fasta_file /path/to/file.fasta \
    --params_nanomonsv_parse "" \
    --params_nanomonsv_get "--min_tumor_variant_read_num 3 --min_tumor_VAF 0.05 --max_control_variant_read_num 0 --max_control_VAF 0.00 --min_indel_size 30 --max_panel_read_num 0 --median_mapQ_thres 20 --qv25"

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.
--params_nanomonsv_parse	Nanomonsv parse parameters (default: ‘““’). Note that the parameters need to be wrapped in quotes.
--params_nanomonsv_get	Nanomonsv get parameters (default: ‘“–min_tumor_variant_read_num 3 –min_tumor_VAF 0.05 –max_control_variant_read_num 0 –max_control_VAF 0.00 –min_indel_size 30 –max_panel_read_num 0 –median_mapQ_thres 20 –qv25”’). Note that the parameters need to be wrapped in quotes.