Provided by: probabel_0.5.0+dfsg-3_amd64
palogist - 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 CHAR Use character CHAR to separate fields in the output file(s) (default is space). -r, --score Use the score test. -e, --no-head Do not report header line in the output. -f --flipmaf Flip reference and effect allele according to Minor Allele Frequency (MAF) such that the minor allele is the effect/predictor allele. If this option is set, ProbABEL will check for each genetic variant whether the Freq1 column in the info file (see the --info option) is > 0.5 and if so will flip the probabilities/dosage of that variant such that A1 and A2 are interchanged. This will add a column called AllelesFlipped to the output file(s), indicating whether the alleles were flipped (1) or not (0). -l --allcov Report estimates for all covariates (large outputs!). -b, --interaction NUMBER Which covariate to use for interaction with SNP analysis (default is no interaction, 0). NUMBER indicates the column number of the covariate. -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! -u, --robust Report robust (a.k.a. sandwich, a.k.a. Hubert-White) standard errors. --help Print help.
The bugtracker is located at https://github.com/GenABEL-Project/ProbABEL/issues
Lennart C. Karssen