Genome-Wide Imputation Pipeline¶
Introduction¶
The genipe (GENome-wide Imputation PipelinE) module provides an easy
and efficient way of performing genome-wide imputation analysis using the three
commonly used tools PLINK,
SHAPEIT and
IMPUTE2.
A database keeps track of all executed steps and enables post-failure relaunch of the pipeline where it last stopped, saving processing time and resources.
A report is automatically generated at the end of the imputation process to easily assess important quality metrics. This report can be rendered to PDF using LaTeX. For information on rendering, refer to this section of the main pipeline tutorial.
Finally, it also provides a useful standalone tool to perform statistical analysis on imputed (dosage) data (such as linear, logistic, repeated measurements, survival analysis, or SKAT). For more information about execution time and important system configuration impacting performance, see the Statistical Analysis Execution Time page.
Usage¶
$ genipe-launcher --help
usage: genipe-launcher [-h] [-v] [--debug] [--thread THREAD] --bfile PREFIX
[--reference FILE] [--chrom CHROM [CHROM ...]]
[--output-dir DIR] [--bgzip] [--use-drmaa]
[--drmaa-config FILE] [--preamble FILE]
[--shapeit-bin BINARY] [--shapeit-thread INT]
[--shapeit-extra OPTIONS] [--plink-bin BINARY]
[--hap-template TEMPLATE] [--legend-template TEMPLATE]
[--map-template TEMPLATE] --sample-file FILE
[--hap-nonPAR FILE] [--hap-PAR1 FILE] [--hap-PAR2 FILE]
[--legend-nonPAR FILE] [--legend-PAR1 FILE]
[--legend-PAR2 FILE] [--map-nonPAR FILE]
[--map-PAR1 FILE] [--map-PAR2 FILE]
[--impute2-bin BINARY] [--segment-length BP]
[--filtering-rules RULE [RULE ...]]
[--impute2-extra OPTIONS] [--probability FLOAT]
[--completion FLOAT] [--info FLOAT]
[--report-number NB] [--report-title TITLE]
[--report-author AUTHOR]
[--report-background BACKGROUND]
Execute the genome-wide imputation pipeline. This script is part of the
'genipe' package, version 1.4.2.
optional arguments:
-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:
--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:
--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:
--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:
--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:
--plink-bin BINARY The Plink binary if it's not in the path.
IMPUTE2 Autosomal Reference:
--hap-template TEMPLATE
The template for IMPUTE2's haplotype files (replace
the chromosome number by '{chrom}', e.g.
'1000GP_Phase3_chr{chrom}.hap.gz').
--legend-template TEMPLATE
The template for IMPUTE2's legend files (replace the
chromosome number by '{chrom}', e.g.
'1000GP_Phase3_chr{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}_combined_b37.txt').
--sample-file FILE The name of IMPUTE2's sample file.
IMPUTE2 Chromosome X Reference:
--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:
--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:
--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:
--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]
Citing genipe¶
If you use genipe in any published work, please cite the paper
describing the tool.
Lemieux Perreault LP, Legault MA, Asselin G, Dubé MP: genipe: an automated genome-wide imputation pipeline with automatic reporting and statistical tools. Bioinformatics 2016, 32 (23): 3661-3663 [DOI:10.1093/bioinformatics/btw487].
About¶
This project was conducted at the Beaulieu-Saucier Pharmacogenomics Centre of the Montreal Heart Institute. The aim was to speed up (and automatize) the imputation process of the whole genome and facilitate downstream data analysis.
