savana

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

usage

nexus run --nf-workflow variant_calling_savana.nf \
    -c nextflow.config \
    -w work/ \
    --samples_tsv_file samples.tsv \
    --output_dir results/ \
    --reference_genome_fasta_file /path/to/file.fasta \
    --custom_params_file /path/to/file \
    --contigs_txt_file /path/to/file.txt \
    --params_savana_run "--length 30 --mapq 20 --min_support 3" \
    --params_savana_classify ""

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.
--custom_params_file	Savana classify –custom_params file.
--contigs_txt_file	TXT file with each contig name in a new line.
--params_savana_run	Savana run parameters (default: ‘“–length 30 –mapq 20 –min_support 3”’). Note that the parameters need to be wrapped in quotes.
--params_savana_classify	Savana classify parameters (default: ‘““’). Note that the parameters need to be wrapped in quotes.