# Wiki

# 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 |
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--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 |
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--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 |
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--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 |
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--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 |
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--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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