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.


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]