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selectionfile.txt
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selectionfile.txt
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#Keyword Parameter Comment
# data files
FILE // Path to SNP/Pedigree/Genotype files. The input format is the standard PLINK (2.2.1) format (map/ped).
TFILE // Path to SNP/Pedigree/Genotype files. The input format is the transposed PLINK (2.2.1) format (tfam/tped).
BFILE // Path to SNP/Pedigree/Genotype files. The input format is the binary PLINK (2.2.1) format (fam/bim/bed).
MAP // Path to the .map file.
PED // Path to the .ped file.
TFAM // Path to the .tfam file.
TPED // Path to the .tped file.
FAM ./test.fam // Path to the .fam file.
BMAP ./test.bim // Path to the .bim file.
BPED ./test.bed // Path to the .bed file.
ANNOTATIONFILE ./data/annotationIlluSorted.txt // path to the annotation file
PATHWAYFILE ./KEGG_2_snp_b129.txt // path to the pathway file
COVARIATEFILE // path to the covariate file
MODELFILE // path to the model file
SNPFILE // path to the SNP file
COMBIFILE // path to the combi file
# selection/reduction of data
SNPLIST 0 // Use only these SNPs for the analysis
COMBILIST 0 // Analyse only pairs or triples from the combi file
ONLY_MALE 0 // 1=only male persons will be analyzed
ONLY_FEMALE 0 // 1=only female persons will be analyzed
POSCHOICE // Selection of certain regions (ONLY the selected region will be analyzed);example:chr4;chr12,123000-160000;chr24;
NEGCHOICE // Exclusion of certain regions (These regions will NOT be analyzed)
MATCHINGCHOICE // Selection of certain regions for pairwise matching
QT 0 // To use the analysis of quantitative traits
MISSING_PHENO -9 // To define the missing phenotype
# output
PRINTTOP 100 // Best n mulitmarker p-values are printed
OUTPUTNAME test_ // Specify the output name
ANNOTATE // Add annotation information in the output files
GENECOL // Specify column number of gene in the annotation information
# quality control
HWE_P_CASE 0.001 // QC-threshold for HWE in cases
HWE_P_CONTROL 0.01 // QC-threshold for HWE in controls
MRDIFF 0.1 // QC-threshold missing rate (mr): individuals and SNPs worse than the average mr + MRDIFF will be deleted
MAF 0 // SNPs with lower MAF are deleted
DOIBS 0 // calculate mean-IBS-status: 0=no, 1=yes, >1=yes and proceed
IBS_SD_RELATIVES // SD-limit for relatives
IBS_SD_OUTLIER // SD-limit for outlier
# single and multi-marker analysis
SINGLE_MARKER 1 // 1=Armitage's trend test, 2=genotype test with 2 d.f., 3=logistic regression 1 d.f., 4=logistic regression 2 d.f.
TWO_MARKER 0 // Two-marker-analysis: 1=yes, 0=no
THREE_MARKER 0 // Three-marker-analysis: 1=yes, 0=no
PRETEST 0 // Pre-test: 1=yes, 0=no
PRETEST_CUTOFF 0.05 // Pre-test threshold
TEST 1 // 1=chi-square-test, 2= log-linear model, 3-12=logistic regression, M=userdefined logistic regression model
COVARIATES // Covariates: all covariates 1-10; or for example 1;8-10;
SEXCOV 0 // 1=sex as a covariate, 0=sex not as a covariate
# priorities
SINGLETOP 500 // Length n of the Single-marker-p-value's toplist
M_WITH_SINGLETOP 0 // number of SNPs(0,1,2,3) which shall be selected from the Single-marker-p-value's toplist
GENETIC_IMPACT 1 // Genetic impact: 0=none (gene desert), 1=close to gene, 2=within gene, 3=within coding region, 4=non-synonymous
M_WITH_GENETIC_IMPACT 0 // Number of SNPs (0,1,2,3) which shall have at least the selected genetic impact
SNP1 // Fix first SNP for analysis; specify rs number
SNP2 // Fix 2ndSNP for analysis; specify rs number
SNP3 // Fix 3rdSNP for analysis (possible only when THREE_MARKER=1); specify rs number
PATHWAY 0 // 1=include pathway information, 0=no
# pathway association analysis
PATHWAYANALYSIS 0 // Pathway association analysis with one of the five pathway association tests
PATHWAYTEST 2 // 1=SNP ratio, 2=Fisher score, 3=gene ratio, 4=Fisher Max), 5= Fisher maxPlus, 6= interaction ratio
P_INTERRATIO 0.5 // p-value cut-off for test 6
# haplotype analysis
HAPLO // Genome-wide Haplotype Analysis (GWHA)
HAPLO_DIST // Define the haplotype distance for pairs/triples
DOHAPFILE // produce proxy-file for YAMAS (section 2.5)
# MC-Simulation
SIMULATION 0 // Number of MC-simulations (0=no simulations will be conducted)
MC_WITH_SM 0 // 1=MC-simulation for multimarker AND singlemarker test. 0=MC-simulation only for multimarker tests.
# Rare Variants
MAFT 0.05 // Set rare MAF threshold
MAF_ADJUST 1 // Correct rare MAF for missings
VT 1 // Optimize rare threshold (variable threshold analysis)
BINSIZE_SNP // Number of SNPs per bin
BINSIZE_RARE 40 // Number of rare SNPs per bin
BINSIZE_DIST // Number of base pairs per bin
RARE_TESTS COLL;CMAT;FR; // Tests to be conducted
GENERATE_SETID // Do not perform analysis; generate SetID file
SETID // Name of SetID file defining the binning
LAMBDA_ADJUST 0 // Lambda p correction for genome-wide FR tests
PRESCREEN 0.0001 // Pretest before simulations are conducted: eliminate bins below (conservative) threshold
ADAPTIVE 0.001 // p-threshold for passing the adaptive permutation method usind Wilson score intervals
MAF_ADJUST 1 // MAF is calculated from expected, (not observed) number of rare alleles in presence of missings. Only used to reduce the number of MAF levels for rare tests, no effect otherwise
INTERVALFILE // data/Ensembl_Genes75_hg19.txt // File containing intervals
INTERVAL_FORMAT // HEAD="1";SEPARATOR="\t";COLUMNS="5";CHR="1";START="2";END="3";FEATURE="4";DESCRIPTION="5"; // Formatting of the interval file
MERGE_INTERVALS // 1 for merging of overlapping intervals from file
FLANKING // Flanking of intervals in bp
CONCATENATE_INTERVALS // Number of consecutive intervals to be concatenated
CLOSE_GAPS // 1 for expanding of intervals to uncovered space
MIN_RARE_IN_BIN // Filter bins: minimum required number of rare SNPs
MAX_RARE_IN_BIN // Maximum allowed number of rare SNPs. Bins split and written to a modified intervalfile.
WEIGHTS // 1/SD | BETA;1;25; | LOGISTIC;0.07;150; Weights of variants for non-collapsing tests (Wu et al. 2011)
VERBOSE 2 // Verbosity level of rare variant analysis
#END