delly2-sr-somatic

Identify somatic variants in paired-end read DNA sequencing BAM files using Delly2

usage

nexus run --nf-workflow variant_calling_delly2-sr-somatic.nf \
    -c nextflow.config \
    -w work/ \
    --samples_tsv_file samples.tsv \
    --output_dir results/ \
    --reference_genome_fasta_file /path/to/file.fasta \
    --exclude_tsv_file /path/to/file.tsv \
    --params_delly2call "--map-qual 20"

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.
--exclude_tsv_file	Delly2 ‘call’ –exclude TSV file.
--params_delly2call	Delly2 ‘call’ parameters (default: ‘“–map-qual 20”’). Note that the parameters need to be wrapped in quotes.