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FAST / Options for running FAST

Option Value Comments
--help - To see all the options described in this table.
--mode genotype/summary MANDATORY option specifying the type of input data.
mode = genotype
--impute2-file File name MANDATORY option for mode = genotype. It specifies the file containing the imputed genotype probabilities in IMPUTE2 format.
--impute2-info-file File name MANDATORY option for mode = genotype. It specifies the file containing the SNP imputation information in IMPUTE2 format.
--tped-file File name MANDATORY option for mode = genotype. It specifies the file containing the genotype dosages for a single chromosome.
--snpinfo-file File name MANDATORY option for mode = genotype. It specifies the file containing the SNP chromosome and positional base-pair information. Must be for a single chromosome sorted in increasing order of base-pair positions.
--mlinfo-file File name MANDATORY option for mode = genotype. It specifies the file containing the SNP allele and imputation quality information. Must be for a single chromosome in same order as the snpinfo-file.
--indiv-file File name MANDATORY option for mode=genotype. This file contains the individual IDs of the samples in the same order as the individuals in the tped-file.
--trait-file File name MANDATORY file for mode=genotype containing the phenotype and optionally, the covariates.
--scale-pheno - For mode=genotype, option to scale the phenotype to have unit variance
--quantile-pheno - For mode=genotype, option to use normal quantile transformation to transform the phenotype to normal distribution
--num-covariates value count of covariates, NOT for Cox models; to include covariates for Cox models, please use "--cox-cov" option (default = 0)
The following three options are for FAST.2.4 ONLY
--cox-strata value count of factors that CoxPH models are stratified on, for Cox methods only (default = 0)
--cox-cov value count of covariates for CoxPH models, for Cox methods only (default = 0)
mode = summary
--summary-file File name MANDATORY option for mode = summary. It specifies the file containing the SNP regression coefficients and standard errors. For methods other than SAPPHO: Must be for a single chromosome sorted in increasing order of base-pair positions. For SAPPHO: could be a combination of multiple chromosomes. Please see input file descriptions for further details.
--multipos-file File name Option for mode = summary. It specifies the file containing the SNPs mapped to multiple positions in the genome. Not needed for SAPPHO methods.
--ld-file File name Option for mode = summary. It specifies the file containing the SNP-SNP LD. For methods other than SAPPHO: this file must be for a single chromosome; must be accompanied by the --allele-file option. Cannot be input when --compute-ld = 1 is specified. For SAPPHO: file can be a combination of multiple chromosomes; if --allele-file is missing, then it is assumed the reference alleles used to calculate LDs were identical to the coding alleles in --summary-file.
--allele-file File name Option for mode = summary. It specifies the file containing the SNP reference allele used in LD computation. For methods other than SAPPHO: Must be for a single chromosome in same order as the --summary-file. If this option is input, the --ld-file option must be also be input. Cannot be input when --compute-ld = 1 is specified. For SAPPHO: this file is not necessarily needed if the reference allele is identical to coding allele; if presented, then SNPs should be in the same order as the --summary-file.
--hap-file File name MANDATORY option for mode = summary when --compute-ld = 1 is specified. When computing LD on the fly, it specifies the input haplotype file. For methods other than SAPPHO: Must be for a single chromosome. If this option is input, the --pos-file option must also be input. For SAPPHO: a haplotype file with multiple chromosomes is needed; all SNPs should be listed first by chromosome number then by BP number; does not need --pos-file.
--pos-file File name MANDATORY option for mode = summary when --compute-ld = 1 is specified. When computing LD on the fly, it specifies the haplotype start byte positions for each haplotype in the file specified with the --hap-file option. Must be for a single chromosome. If this option is input, the --hap-file option must be also be input. Not needed for SAPPHO.
--pheno-var value For mode=summary option, specifying phenotype variance for methods other than SAPPHO.
--pheno-varcov-file File name Option for mode = summary, file specifying the variance-covariance for SAPPHO. If not present then SAPPHO will calculate it from --summary-file.
--compute-ld 0/1 For mode=summary, option to compute LD on the fly (default = no). If this option is specified, --hap-file and --pos-file must also be present when mode=summary for methods other than SAPPHO. For SAPPHO, --hap-file is only needed to compute LD on the fly.
--n-sample value For mode=summary MANDATORY option specifying number of samples/individuals to be used in the analysis. Not needed for SAPPHO.
Input options common for both modes
--chr chromosome number MANDATORY chromosome number for either mode. It should be same as the chromosome number specified in the above input files for either mode. Valid values are 1-22 for autosomal chromosomes and 23 for chromosome X.
--out-file Filename Output files are prefixed with filename, default = FAST.result
--gene-set filename File containing gene names and boundaries for either mode. If not specified, FAST will perform single SNP analysis.
--maf-cutoff value value to filter snps with maf < maf-cutoff for gene-based analysis (default = 0.01)
--random-seed value Seed for permutations (default = 2)
--flank value upstream and downstream gene flanking region in base-pairs (default = 20000 bp)
--max-perm value max no. of permutations (default = 1000000)
--n-perm-min value min no. of permutations (default = 100)
--max-missingness value Fraction indicating max allowed missingness per snp (default = 0.05)
--missing-val value For mode = genotype, value indicating missing genotypes (default = -1)
--eff-sample-size value min effective sample size per snp for gene based analysis (default = 5)
--imputation-quality value min imputation quality per snp for gene based analysis (default = 0.3)
--omit-strand-ambiguous - drop strand ambiguous snps (default = no)
--skip-perm - If specified no permutations will be performed.
--verbose - Detailed output for debugging (default = no)
--n-threads value No. of threads / multiple cores in permutations (default = 1)
--sigma-a value priors for additive effects in Bayes Factor computations (default = 0.2)
The following three options are for FAST.2.4 ONLY
--num-phenotypes value count of phenotypes for SAPPHO analysis, for SAPPHO methods only (default = 1)
--sappho-alpha value tuning parameter for SAPPHO model prior, should be a number between 0 and 1. Usually left as default.
Linear Regression Based Analysis Options For more description of the methods, please refer to the Output File Format Session
--linear-snp - single snp linear regression for all snps
--linear-snp-gene - single snp linear regression for only the snps in the genes
--linear-minsnp - linear regression based minsnp
--linear-minsnp-gene-perm - linear regression based minsnp-gene-perm
--linear-gwis - linear regression based GWiS (i.e. GWiS-Linear)
--linear-bf - linear regression based Bayes Factors (Bimbam)
--linear-vegas - linear regression based Vegas
--linear-gates - linear regression based Gates
--linear-minsnp-perm - linear regression based minsnp with permutation pvalues
--linear-gwis-perm - linear regression based GWiS with permutation pvalues
--linear-bf-perm - linear regression based Bayes Factors with permutation pvalues
--linear-vegas-perm - linear regression based Vegas with permutation pvalues
Logistic Regression Based Analysis Options For more description of the methods, please refer to the Output File Format Session
--logistic-snp - single snp logistic regression for all snps
--logistic-snp-gene - single snp logistic regression for only the snps in the genes
--logistic-minsnp - logistic regression based minsnp
--logistic-minsnp-gene-perm - logistic regression based minsnp--perm
--logistic-gwis - logistic regression based GWiS (i.e. GWiS-Logistic)
--logistic-bf - logistic regression based Bayes Factors
--logistic-vegas - logistic regression based Vegas
--logistic-gates - logistic regression based Gates
--logistic-minsnp-perm - logistic regression based minsnp with permutation pvalues
--logistic-gwis-perm - logistic regression based GWiS with permutation pvalues
--logistic-bf-perm - logistic regression based Bayes Factors with permutation pvalues
--logistic-vegas-perm - logistic regression based Vegas with permutation pvalues
Other Regression Based Options For more description of the methods, please refer to the Output File Format Session
--sapphoI - sapphoI model for pleiotropy regression
--sapphoC - sapphoC model for pleiotropy regression
--cox-snp - single SNP Cox Proportional Hazard test
--cox-gene - gene-based Cox Proportional Hazard test in GWiS-like score framework

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