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• Impute2 Merger - impute2-merger

  • General options

  • Input files

  • Options

  • Output files

Impute2 Merger - impute2-merger

Concatenate IMPUTE2 output files and retrieve some statistics. This tool is automatically called by the main genipe pipeline to merge IMPUTE2 files generated for all the genomic segments (see IMPUTE2 merger options).

General options

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

Option		Description
--impute2 FILE [FILE ...] | The output from IMPUTE2.

Options

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

Option	Description
--prefix FILE	The prefix for the output files. [imputed]