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:
    tools_ngs_mapping: []  # optional, copied from ngs mapping config
    tools_variant_calling: []  # optional, copied from variant calling config
    path_variant_calling: ../variant_calling  # REQUIRED
    tools: ['peddy']  # REQUIRED - available: '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.