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• Imputed Stats - imputed-stats

  • Available statistical models

  • Common options

    • General options

    • Input files

    • Output options

    • General options

    • Dosage options

    • Phenotype options

  • Cox’s proportional hazard model options

  • Linear regression options

  • Logistic regression options

  • Linear mixed effects options

  • SKAT options

Imputed Stats - imputed-stats

Performs statistical analysis on imputed data (either SKAT analysis, or linear, logistic or survival regression).

Available statistical models

Name	Description
cox	Cox’s proportional hazard model (survival regression).
linear	Linear regression (ordinary least squares).
logistic	Logistic regression (GLM with binomial distribution).
mixedlm	Linear mixed effect model (random intercept).
skat	SKAT analysis.

Common 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	The output from IMPUTE2.
--sample FILE	The sample file (the order should be the same as in the IMPUTE2 files).
--pheno FILE	The file containing phenotypes and co variables.
--extract-sites FILE	A list of sites to extract for analysis (optional).

Output options

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

General options

Option	Description
--nb-process INT	The number of process to use. [1]
--nb-lines INT	The number of line to read at a time. [1000]
--chrx	The analysis is performed for the non pseudo-autosomal region of the chromosome X (male dosage will be divided by 2 to get values [0, 0.5] instead of [0, 1]) (males are coded as 1 and option ‘--gender-column’ should be used).
--gender-column NAME	The name of the gender column (use to exclude samples with unknown gender (i.e. not 1, male, or 2, female). If gender not available, use ‘None’. [Gender]

Dosage options

Option	Description
--scale INT	Scale dosage so that values are in [0, n] (possible values are 1 (no scaling) or 2). [2]
--prob FLOAT	The minimal probability for which a genotype should be considered. [>=0.9]
--maf FLOAT	Minor allele frequency threshold for which marker will be skipped. [<0.01]

Phenotype options

Option	Description
--covar NAME	The co variable names (in the phenotype file), separated by coma.
--categorical NAME	The name of the variables that are categorical (note that the gender is always categorical). The variables are separated by coma.
--missing-value NAME	The missing value in the phenotype file.
--sample-column NAME	The name of the sample ID column (in the phenotype file). [sample_id]
--interaction NAME	Add an interaction between the genotype and this variable.

Cox’s proportional hazard model options

Option	Description
--time-to-event NAME	The time to event variable (in the pheno file).
--event NAME	The event variable (1 if observed, 0 if not observed).

Linear regression options

Option	Description
--pheno-name NAME	The phenotype.

Logistic regression options

Option	Description
--pheno-name NAME	The phenotype.

Linear mixed effects options

Option	Description
--pheno-name NAME	The phenotype.
--use-ml	Fit the standard likelihood using maximum likelihood (ML) estimation instead of REML (default is REML).
--p-threshold FLOAT	The p-value threshold for which the real MixedLM analysis will be performed. [<0.0001]

SKAT options

Option	Description
--snp-sets FILE	A file indicating a snp_set and an optional weight for every variant.
--outcome-type {continuous,discrete}	The variable type for the outcome. This will be passed to SKAT.
--skat-o	By default, the regular SKAT is used. Setting this flag will use the SKAT-O algorithm instead.
--pheno-name NAME	The phenotype.