pbsv

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

usage

nexus run --nf-workflow variant_calling_pbsv.nf \
    -c nextflow.config \
    -w work/ \
    --samples_tsv_file samples.tsv \
    --output_dir results/ \
    --reference_genome_fasta_file /path/to/file.fasta \
    --params_pbsv_discover "--ccs --min-gap-comp-id-perc 97 --min-mapq 20" \
    --params_pbsv_call "--ccs --call-min-reads-per-strand-all-samples 0 --call-min-read-perc-one-sample 10 --call-min-reads-all-samples 3 --call-min-reads-one-sample 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’, ‘bam_file’, ‘bam_bai_file’.
--output_dir	Directory to which output files will be copied.
--reference_genome_fasta_file	Reference genome FASTA file.
--params_pbsv_discover	Pbsv ‘discover’ parameters (default: ‘“–ccs –min-gap-comp-id-perc 97 –min-mapq 20”’). Note that the parameters need to be wrapped in quotes.
--params_pbsv_call	Pbsv ‘call’ parameters (default: ‘“–ccs –call-min-reads-per-strand-all-samples 0 –call-min-read-perc-one-sample 10 –call-min-reads-all-samples 3 –call-min-reads-one-sample 3”’). Note that the parameters need to be wrapped in quotes.