sequenza

Identify somatic copy number variants in paired-end read DNA sequencing BAM files using Sequenza

usage

nexus run --nf-workflow variant_calling_sequenza.nf \
    -c nextflow.config \
    -w work/ \
    --samples_tsv_file samples.tsv \
    --output_dir results/ \
    --reference_genome_fasta_file /path/to/file.fasta \
    --assembly "" \
    --sequenzautils_gcwiggle "-w 50" \
    --sequenzautils_bam2seqz "-N 20 --qformat sanger" \
    --sequenzautils_seqzbinning "--window 50" \
    --chromosomes "chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 ch22 chrX chrY"

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.
--assembly	Assembly (‘hg19’ or ‘hg38’).
--chromosomes	List of chromosomes (default: ‘“chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 ch22 chrX chrY”’). Note that the parameters need to be wrapped in quotes.
--params_sequenzautils_gcwiggle	sequenza-utils ‘gc_wiggle’ parameters (default: ‘“-w 50”’). Note that the parameters need to be wrapped in quotes.
--params_sequenzautils_bam2seqz	sequenza-utils ‘bam2seqz’ parameters (default: ‘“-N 20 –qformat sanger”’). Note that the parameters need to be wrapped in quotes.
--params_sequenzautils_seqzbinning	sequenza-utils ‘seqz_binning’ parameters (default: ‘“–window 50”’). Note that the parameters need to be wrapped in quotes.