octopus-germline

Identify germline variants in paired-end read DNA sequencing BAM files using Octopus

usage

nexus run --nf-workflow variant_calling_octopus-germline.nf \
    -c nextflow.config \
    -w work/ \
    --samples_tsv_file samples.tsv \
    --output_dir results/ \
    --reference_genome_fasta_file /path/to/file.fasta \
    --regions_txt_file /path/to/file.txt \
    --params_octopus "--min-mapping-quality 20 --min-supporting-reads 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 symlinked.
--reference_genome_fasta_file	Reference genome FASTA file.
--params_octopus	Octopus germline mode parameters (default: ‘“–min-mapping-quality 20 –min-supporting-reads 3”’). Note that the parameters need to be wrapped in quotes.