Variant Calling (Long-read DNA Somatic)

Identify somatic DNA variants in long-read DNA sequencing BAM files

tools

The following tools run by default (methods: "all"):

clairs, deepsomatic, delly2, dysgu, nanomonsv, savana, severus, svisionpro

usage

nexus run --nf-workflow variant_calling_long-read-dna-somatic.nf -params-file params.yaml

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

Download params.yaml

# =============================================================================
# params.yaml — variant_calling_long-read-dna-somatic
#
# Usage:
#   nextflow run variant_calling_long-read-dna-somatic.nf -params-file params.yaml
#
# Fill in the required fields below. Optional fields can be left at their
# defaults or removed entirely.
# =============================================================================


# -----------------------------------------------------------------------------
# Required
# -----------------------------------------------------------------------------

# TSV file with columns:
#   sample_id
#   tumor_bam_file
#   tumor_bam_bai_file
#   normal_bam_file
#   normal_bam_bai_file
#   normal_small_variants_vcf_file   (required for Severus; normal DeepVariant VCF
#                                     from variant_calling_long-read-dna-germline output;
#                                     will be phased by WhatsHap before Severus)
samples_tsv_file: ""

# Directory to which output files will be copied
output_dir: ""

# Reference genome FASTA file
reference_genome_fasta_file: ""


# -----------------------------------------------------------------------------
# Optional — general
# -----------------------------------------------------------------------------

# Methods to run. Comma-separated list or 'all'.
# Allowed values:
#   all, clairs, deepsomatic, delly2, dysgu, nanomonsv,
#   savana, severus, svisionpro
methods: "all"


# -----------------------------------------------------------------------------
# ClairS
# Optional arguments.
# -----------------------------------------------------------------------------
clairs:
  # Extra CLI arguments passed directly to ClairS.
  extra_args: "--platform hifi_revio --enable_indel_calling"


# -----------------------------------------------------------------------------
# DeepSomatic
# Required when methods includes 'deepsomatic' or 'all':
#   input_path, output_path
# Optional otherwise.
# -----------------------------------------------------------------------------
deepsomatic:
  # Required when running DeepSomatic
  input_path: ""
  output_path: ""

  # Containerization engine: 'singularity' or 'docker'
  containerization: "singularity"

  # DeepSomatic --model_type value
  model_type: "PACBIO"

  # Path to the run_deepsomatic binary
  bin_path: "run_deepsomatic"

  # DeepSomatic version
  bin_version: "1.9.0"


# -----------------------------------------------------------------------------
# Delly2
# Required when methods includes 'delly2' or 'all':
#   exclude_tsv_file
# Optional otherwise.
# -----------------------------------------------------------------------------
delly2:
  # Required when running Delly2
  exclude_tsv_file: ""

  # Extra CLI arguments passed directly to delly2 lr.
  extra_args: "--mapqual 20 --technology pb"


# -----------------------------------------------------------------------------
# Dysgu
# Optional arguments.
# -----------------------------------------------------------------------------
dysgu:
  # Extra CLI arguments passed directly to dysgu run.
  run_extra_args: "--mode pacbio-revio --min-support 3 --min-size 30 --mq 20"

  # Extra CLI arguments passed directly to dysgu filter.
  filter_extra_args: "--support-fraction 0.05 --min-mapq 20 --pass-prob 0.2"


# -----------------------------------------------------------------------------
# nanomonsv
# Optional arguments.
# -----------------------------------------------------------------------------
nanomonsv:
  # Extra CLI arguments passed directly to nanomonsv parse.
  parse_extra_args: ""

  # Extra CLI arguments passed directly to nanomonsv get.
  get_extra_args: ""


# -----------------------------------------------------------------------------
# Savana
# Required when methods includes 'savana' or 'all':
#   contigs_txt_file, custom_params_file
# Optional otherwise.
# -----------------------------------------------------------------------------
savana:
  # Required when running Savana
  contigs_txt_file: ""
  custom_params_file: ""

  # Extra CLI arguments passed directly to savana run.
  run_extra_args: "--length 30 --mapq 20 --min_support 3"

  # Extra CLI arguments passed directly to savana classify.
  classify_extra_args: ""


# -----------------------------------------------------------------------------
# Severus
# Required when methods includes 'severus' or 'all':
#   vntr_bed_file
# Optional otherwise.
# -----------------------------------------------------------------------------
severus:
  # Required when running Severus
  vntr_bed_file: ""

  # Extra CLI arguments passed directly to severus.
  extra_args: ""

  # Extra CLI arguments passed directly to whatshap phase (for phasing normal VCF).
  whatshap_extra_args: ""


# -----------------------------------------------------------------------------
# SVision-pro
# Required when methods includes 'svisionpro' or 'all':
#   model_file
# Optional otherwise.
# -----------------------------------------------------------------------------
svisionpro:
  # Required when running SVision-pro
  model_file: ""

  # Extra CLI arguments passed directly to SVision-pro.
  extra_args: ""

  # Extra CLI arguments passed directly to SVision-pro extract.
  extract_extra_args: ""