Configuration

Configuration

TeddyPi is configured with configuration files in the YAML format ( yaml.org ). The main configuration is in teddypi.yaml stores the list of samples,list of programs and some parameters.

Example:

# teddypi.yaml
samples: testA, testB, testC
ortho_merge_distance: 50

For each TE/SV callers an additional configuration file must be provided, that stores general information about the data supplied by the caller and the filtering pipeline to be utilized.

Filters are supplied as list after filters:, each list element can contain muliple lines with key:value assignments. The filters are applied by TeddyPi in ascending order given by the order key. The method field refers to method defined in the VCFfilters class in tpi_filters.py. By implementing or changing methods, TeddyPi can easily be adapted with new filters or meet requirements for additional or novel TE and SV callers.

Example:

name: Pindel
rel: ref # ref or nonref (Ref+ / Ref-)
type: DEL # TE or DEL
filters:
- name: FILTER_1 # Name to identify filter
  order: 01 # This is the first filter step
  method: retroseq_gt_hom # call this method from tpi_filter.py
- name: FILTER_2
  order: 02
  method: method_xyz # another method defined in tpi_filter.py
  additional_key: value # additional parameters for the method