Germline Variant Annotation

Implementation of the variant_annotation step

The variant_annotation step takes as the input the results of the variant_calling step (called germline variants in vcf.gz format) and annotates the variants, e.g., using VEP.

Stability

TBD

Step Input

The variant annotation step uses Snakemake sub workflows for using the result of the variant_calling step.

Step Output

TBD

Global Configuration

TBD

Default Configuration

The default configuration is as follows.

# Default configuration variant_annotation
step_config:
  variant_annotation:
    path_variant_calling: ../variant_calling
    tools:
      - vep
    vep:
      # We will always run VEP in cache mode.  You have to provide the directory to the
      # cache to use (VEP would be ``~/.vep``).
      cache_dir: null # OPTIONAL
      # The cache version to use.  gnomAD v2 used 85, gnomAD v3.1 uses 101.
      cache_version: "85"
      # The assembly to use.  gnomAD v2 used "GRCh37", gnomAD v3.1 uses "GRCh38".
      assembly: "GRCh37"
      # The flag selecting the transcripts.  One of "gencode_basic", "refseq", and "merged".
      tx_flag: "gencode_basic"
      # Number of threads to use with forking, set to 0 to disable forking.
      num_threads: 16
      # Additional flags.
      more_flags: "--af_gnomade --af_gnomadg"
      # The --buffer_size parameter
      buffer_size: 100000

Available Variant Annotators

The following variant annotator is currently available:

Reports

N/A