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"
– callbcftools stats
for various statistics"peddy"
– check variants against a PED file
Reports
Currently, no reports are generated.