Configuration

Main 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

Filter configuration

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.

Each filter block starts with a hyphen -, and several key: value pairs. The name, order, and method fields are mandatory. They give the filter a unique name, that appears in the program routine and output, the order of execution in ascending numbers and the method that is called from the program code.

Example:

- name: FILTER_1 # Name to identify filter
  order: 01 #
  method: retroseq_gt_hom # call this method from tpi_filter.py

Optionally, arguments to filter-method (if it takes any) can be given. For example, the following filter selected for VCF entries matching the string SINE using the meinfo_type method. Example

- name: SINE
  order: 00
  method: meinfo_type
  type: SINE

Finally, filters can be deactivated without removing fronm the configuration file by adding deactivate: True.