dysgu-somatic

Identify somatic structural variants in long-read or paired-end DNA sequencing BAM files using Dysgu

usage

nexus run --nf-workflow variant_calling_dysgu-somatic.nf \
    -c nextflow.config \
    -w work/ \
    --samples_tsv_file samples.tsv \
    --output_dir results/ \
    --reference_genome_fasta_file /path/to/file.fasta \
    --params_dysgu_run "--mode pacbio-revio --min-support 3 --min-size 30 --mq 20" \
    --params_dysgu_filter "--support-fraction 0.05 --min-mapq 20 --pass-prob 0.2"

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_dysgu_run	Dysgu run parameters (default: ‘“–mode pacbio-revio –min-support 3 –min-size 30 –mq 20”’). Note that the parameters need to be wrapped in quotes.
--params_dysgu_filter	Dysgu filter parameters (default: ‘“–support-fraction 0.05 –min-mapq 20 –pass-prob 0.2”’). Note that the parameters need to be wrapped in quotes.