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ehdn-to-eh

In order to transform the output from ExpansionHunter Denovo (EHdn) into a variant catalog usable for ExpansionHunter (EH), the scripts in 'create_variant_vatalog.py' can be used. EHdn has two modes of analysis, for which a different function is needed. In case of the

  • outlier analysis, use function: 'transform_outlier_format'.
  • casecontrol analysis, use function: 'transform_casecontrol_format'.

These functions take the input- and output files as arguments, using the following parameters:

  • ehdn_file: the file as outputted by EHdn (tsv format).
  • refgen_file: the file containing the reference genome, used for the EHdn analysis (fasta format).
  • varcat_out_file: the filename used for the variant catalog output file.
  • unmatched_out_file: the filename used for the unmatched regions output file; i.e. the regions that have no repeats in the reference genome.
  • excluded_out_file: the filename used for the excluded regions output file; i.e. the regions that contain more than 5 N's in the reference genome (EH doesn't accept these regions).

The outputs will be written to the specified output files.