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• Main Pipeline - genipe-launcher

  • General options

  • Input options

  • Output options

  • HPC options

  • SHAPEIT options

  • Plink options

  • IMPUTE2 autosomal reference

  • IMPUTE2 chromosome X reference

  • IMPUTE2 options

  • IMPUTE2 merger options

  • Automatic report options

Main Pipeline - genipe-launcher

Execute the genome-wide imputation pipeline.

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.
--thread THREAD	Number of threads [1].

Input options

Option	Description
--bfile PREFIX	The prefix of the binary pedfiles (input data).
--reference FILE	The human reference to perform an initial strand check (useful for genotyped markers not in the IMPUTE2 reference files) (optional).

Output options

Option	Description
--chrom CHROM [CHROM ...]	The chromosomes to process. It is possible to write ‘autosomes’ to process all the autosomes (from chromosome 1 to 22, inclusively).
--output-dir DIR	The name of the output directory. [genipe]
--bgzip	Use bgzip to compress the impute2 files.

HPC options

Option	Description
--use-drmaa	Launch tasks using DRMAA.
--drmaa-config FILE	The configuration file for tasks (use this option when launching tasks using DRMAA). This file should describe the walltime and the number of nodes/processors to use for each task.
--preamble FILE	This option should be used when using DRMAA on a HPC to load required module and set environment variables. The content of the file will be added between the ‘shebang’ line and the tool command.

SHAPEIT options

Option	Description
--shapeit-bin BINARY	The SHAPEIT binary if it’s not in the path.
--shapeit-thread INT	The number of thread for phasing. [1]
--shapeit-extra OPTIONS	SHAPEIT extra parameters. Put extra parameters between single or normal quotes (e.g. --shapeit-extra '-- states 100 --window 2').

Plink options

Option	Description
--plink-bin BINARY	The Plink binary if it’s not in the path.

IMPUTE2 autosomal reference

Option	Description
--hap-template TEMPLATE	The template for IMPUTE2’s haplotype files (replace the chromosome number by ‘{chrom}’, e.g. ‘1000GP_{chrom}.hap.gz’).
--legend-template TEMPLATE	The template for IMPUTE2’s legend files (replace the chromosome number by ‘{chrom}’, e.g. ‘1000GP_{chrom}.legend.gz’).
--map-template TEMPLATE	The template for IMPUTE2’s map files (replace the chromosome number by ‘{chrom}’, e.g. ‘genetic_map_chr{chrom}.txt’).
--sample-file FILE	The name of IMPUTE2’s sample file.

IMPUTE2 chromosome X reference

Option	Description
--hap-nonPAR FILE	The IMPUTE2’s haplotype file for the non-pseudoautosomal region of chromosome 23.
--hap-PAR1 FILE	The IMPUTE2’s haplotype file for the first pseudoautosomal region of chromosome 23.
--hap-PAR2 FILE	The IMPUTE2’s haplotype file for the second pseudoautosomal region of chromosome 23.
--legend-nonPAR FILE	The IMPUTE2’s legend file for the non-pseudoautosomal region of chromosome 23.
--legend-PAR1 FILE	The IMPUTE2’s legend file for the first pseudoautosomal region of chromosome 23.
--legend-PAR2 FILE	The IMPUTE2’s legend file for the second pseudoautosomal region of chromosome 23.
--map-nonPAR FILE	The IMPUTE2’s map file for the non-pseudoautosomal region of chromosome 23.
--map-PAR1 FILE	The IMPUTE2’s map file for the first pseudoautosomal region of chromosome 23.
--map-PAR2 FILE	The IMPUTE2’s map file for the second pseudoautosomal region of chromosome 23.

IMPUTE2 options

Option	Description
--impute2-bin BINARY	The IMPUTE2 binary if it’s not in the path.
--segment-length BP	The length of a single segment for imputation. [5e+06]
--filtering-rules RULE [RULE ...]	IMPUTE2 filtering rules (optional).
--impute2-extra OPTIONS	IMPUTE2 extra parameters. Put the extra parameters between single or normal quotes (e.g. --impute2-extra '-buffer 250 -Ne 20000').

IMPUTE2 merger options

Option	Description
--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]

Automatic report options

Option	Description
--report-number NB	The report number. [genipe automatic report]
--report-title TITLE	The report title. [genipe: Automatic genome-wide imputation]
--report-author AUTHOR	The report author. [Automatically generated by genipe]
--report-background BACKGROUND	The report background section (can either be a string or a file containing the background. [General background]