.. contents:: Quick navigation :depth: 2 Impute2 Merger - ``impute2-merger`` ==================================== Concatenate *IMPUTE2* output files and retrieve some statistics. This tool is automatically called by the main :py:mod:`genipe` pipeline to merge *IMPUTE2* files generated for all the genomic segments (see :ref:`main-pipeline-merger-options`). General options ---------------- .. table:: +-----------------------+-------------------------------------------------+ | Option | Description | +=======================+=================================================+ | ``-h``, ``--help`` | Show this help message and exit. | +-----------------------+-------------------------------------------------+ | ``-v``, ``--version`` | Show program's version number and exit. | +-----------------------+-------------------------------------------------+ | ``--debug`` | Set the logging level to debug. | +-----------------------+-------------------------------------------------+ Input files ------------ .. table:: +-------------------------------+-----------------------------------------+ | Option | Description | +===============================+=========================================+ | ``--impute2 FILE [FILE ...]`` | The output from IMPUTE2. | +--------------------+----------------------------------------------------+ Options -------- .. table:: +-------------------------+-----------------------------------------------+ | Option | Description | +=========================+===============================================+ | ``--chr CHR`` | The chromosome on witch the imputation was | | | made. | +-------------------------+-----------------------------------------------+ | ``--probability FLOAT`` | The probability threshold for no calls. | | | [``<0.9``] | +-------------------------+-----------------------------------------------+ | ``--completion FLOAT`` | The completion rate threshold for site | | | exclusion. [``<0.98``] | +-------------------------+-----------------------------------------------+ | ``--info FLOAT`` | The measure of the observed statistical | | | information associated with the allele | | | frequency estimate threshold for site | | | exclusion. [``<0.00``] | +-------------------------+-----------------------------------------------+ Output files ------------- .. table:: +-------------------+-----------------------------------------------------+ | Option | Description | +===================+=====================================================+ | ``--prefix FILE`` | The prefix for the output files. [``imputed``] | +-------------------+-----------------------------------------------------+