Wiki
Clone wikiFAST / 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 |
Updated