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.

step_config:
  variant_annotation:

    # Path to variant calling
    #path_variant_calling: ../variant_calling          # Examples: ../variant_calling
    #tools:                                            # Options: 'vep'
    #  - vep
    #vep:
    #
    #  # Defaults to $HOME/.vep Not a good idea on the cluster
    #  cache_dir: ''
    #  species: homo_sapiens
    #
    #  # The assembly to use.  gnomAD v2 used "GRCh37", gnomAD v3.1 uses "GRCh38".
    #  assembly: GRCh37
    #
    #  # The cache version to use.  gnomAD v2 used 85, gnomAD v3.1 uses 101.
    #  cache_version: '85'
    #
    #  # The flag selecting the transcripts.  One of "gencode_basic", "refseq", and "merged".
    #  tx_flag: gencode_basic                          # Options: 'gencode_basic', 'refseq', 'merged'
    #  pick_order:
    #    - biotype
    #    - mane
    #    - appris
    #    - tsl
    #    - ccds
    #    - canonical
    #    - rank
    #    - length
    #  num_threads: 16
    #  buffer_size: 100000
    #  output_options:
    #    - everything
    #  more_flags: --af_gnomade --af_gnomadg

Available Variant Annotators

The following variant annotator is currently available:

Reports

N/A