Germline Variant Sanity Checking

Implementation of the germline variant_checking step

The variant_checking step takes as the input the results of the variant_annotation step. It then executes various tools computing statistics on the result files and consistency checks with the pedigrees.

Step Input

The variant calling step uses Snakemake sub workflows for using the result of the variant_annotation step.

Step Output

Note

TODO

Global Configuration

Note

TODO

Default Configuration

The default configuration is as follows.

step_config:
  variant_checking:

    # copied from ngs mapping config
    #tools_ngs_mapping: []
    #
    # copied from variant calling config
    #tools_variant_calling: []
    #
    # Path to variant calling
    path_variant_calling:                             # REQUIRED; Examples: ../variant_calling
    #tools:                                            # Options: 'peddy'
    #  - peddy

Available Variant Checkers

The following variant checkers integrated:

  • "bcftools_stats" – call bcftools stats for various statistics

  • "peddy" – check variants against a PED file

Reports

Currently, no reports are generated.