Variant Calling (Short-read DNA Germline)

Identify germline DNA variants in short-read DNA sequencing BAM files

tools

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

clair3, deepvariant, delly2, dysgu, gridss2, haplotypecaller, lumpy, manta, octopus, pindel, strelka2

usage

nexus run --nf-workflow variant_calling_short-read-dna-germline.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_short-read-dna-germline
#
# Usage:
#   nextflow run variant_calling_short-read-dna-germline.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
#   bam_file
#   bam_bai_file
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, clair3, deepvariant, delly2, dysgu, gridss2,
#   haplotypecaller, lumpy, manta, octopus, pindel, strelka2
methods: "all"


# -----------------------------------------------------------------------------
# Clair3
# Optional arguments.
# -----------------------------------------------------------------------------
clair3:
  # Extra CLI arguments passed directly to Clair3.
  extra_args: "--model_path=/opt/models/ilmn/ --platform=ilmn --min_coverage=3"


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

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

  # DeepVariant --model_type value
  model_type: "WGS"

  # Path to the run_deepvariant binary
  bin_path: "/opt/deepvariant/bin/run_deepvariant"

  # DeepVariant 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 call.
  extra_args: "--map-qual 20"


# -----------------------------------------------------------------------------
# Dysgu
# Optional arguments.
# -----------------------------------------------------------------------------
dysgu:
  # Extra CLI arguments passed directly to dysgu run.
  run_extra_args: "--mode pe --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"


# -----------------------------------------------------------------------------
# GRIDSS2
# Optional arguments.
# -----------------------------------------------------------------------------
gridss2:
  # Extra CLI arguments passed directly to gridss.
  extra_args: ""


# -----------------------------------------------------------------------------
# HaplotypeCaller
# Optional arguments.
# -----------------------------------------------------------------------------
haplotypecaller:
  # Extra CLI arguments passed directly to GATK4 HaplotypeCaller.
  extra_args: ""

  # Chromosomes (for compute parallelization purposes)
  chromosomes: "chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chrX,chrY"


# -----------------------------------------------------------------------------
# Manta
# Optional arguments.
# -----------------------------------------------------------------------------
manta:
  # Extra CLI arguments passed directly to configManta.py.
  config_extra_args: ""

  # Extra CLI arguments passed directly to runWorkflow.py.
  run_extra_args: ""


# -----------------------------------------------------------------------------
# Octopus
# Required when methods includes 'octopus' or 'all':
#   regions_txt_file
# Optional otherwise.
# -----------------------------------------------------------------------------
octopus:
  # Required when running Octopus
  regions_txt_file: ""

  # Extra CLI arguments passed directly to octopus.
  extra_args: "--min-mapping-quality 20 --min-supporting-reads 3"


# -----------------------------------------------------------------------------
# Pindel
# Optional arguments.
# -----------------------------------------------------------------------------
pindel:
  # Extra CLI arguments passed directly to pindel.
  extra_args: ""


# -----------------------------------------------------------------------------
# Strelka2
# Optional arguments.
# -----------------------------------------------------------------------------
strelka2:
  # Extra CLI arguments passed directly to configureStrelkaGermlineWorkflow.py.
  extra_args: ""