palogist(1) Perform Genome-Wide Association Analysis using a logistic model


palogist [ command-line options ]


palogist runs a linear regression on large imputed data sets in an efficient way.


Required command line options

-p, --pheno FILE
Read phenotype data from FILE
-i, --info FILE
Read SNP information from FILE (e.g. MLINFO file).
-d, --dose FILE
SNP predictor (e.g. MLDOSE/MLPROB) file name.

Optional command line options

-m, --map FILE
Map file name, containing base pair positions for each SNP.
-n, --nids NUMBER
Number of people to analyse.
-c, --chrom FILE
Chromosome (to be passed to output).
-o, --out FILE
Output file name (default is regression.out.txt ).
-s, --skipd NUMBER
How many columns to skip in predictor (dose/prob) file (default is 2).
-t, --ntraits NUMBER
How many traits are analysed (default is 1).
-g, --ngpreds NUMBER
How many predictor columns per marker (default 1 = MLDOSE; else use 2 for MLPROB).
-a, --separat FILE
Character to separate fields (default is space).
-r, --score
Use the score test.
-e, --no-head
Do not report header line in the output.
-l --allcov
Report estimates for all covariates (large outputs!).
-b, --interaction
Which covariate to use for interaction with SNP analysis (default is no interaction, 0).
-k, --interaction_only
Like --interaction but without covariate acting in interaction with SNP (default is no interaction, 0).
-v, --mmscore FILE
Score test in samples of related individuals. The FILE argument is the name of a file with the inverse correlation matrix. NOTE THAT THIS FEATURE IS STILL EXPERIMENTAL!
Report robust (a.k.a. sandwich, a.k.a. Hubert-White) standard errors.
Print help.


The bugtracker is located at


Lennart C. Karssen