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Sample scripts for running FAST with typical options
With Summary Data
All methods using Case-Control (i.e. dichotomous) phenotype with logistic regression, LD computed on the fly for each chromosome.
#!/bin/bash # This script will run FAST in mode=summary with LD computed on the fly and basic set of inputs. # The input is from files in DATA.summary # The output is stored in OUT time ./FAST \ --summary-file ./DATA.summary/chr1.simple \ --hap-file ./DATA.summary/chr1.hap \ --pos-file ./DATA.summary/chr1.hap.ra \ --out-file ./OUT/output6 \ --gene-set ./DATA.summary/genes.txt \ --chr 1 \ --mode summary \ --n-sample 2000 \ --logistic-minsnp-perm \ --logistic-minsnp-gene-perm \ --logistic-vegas-perm \ --logistic-gates \ --logistic-gwis-perm \ --logistic-bf-perm
All methods using Summary data with pre-computed LD files for each chromosome, quantitative phenotype
#!/bin/bash # This script will run FAST in mode=summary with pre-computed ld files. # The input is from files in DATA.summary # The output is stored in OUT for CHR in {1..22} do time ./FAST \ --summary-file ./DATA.summary/chr$CHR.summary \ --multipos-file ./DATA.summary/chr$CHR.multiPos.txt \ --ld-file ./DATA.summary/chr$CHR.ld \ --allele-file ./DATA.summary/chr$CHR.allele.info \ --out-file ./OUT/output \ --gene-set ./DATA.summary/genes_list.txt \ --chr $CHR \ --pheno-var 0.1875 \ --n-sample 2000 \ --mode summary \ --maf-cutoff 0.01 \ --max-perm 1000000\ --linear-minsnp-perm \ --linear-minsnp-gene-perm \ --linear-vegas-perm \ --linear-gates \ --linear-gwis-perm \ --linear-bf-perm done
With Genotype data
All methods using linear regression model
#!/bin/bash # This script will run FAST in mode=genotype with linear model on all 22 chromosomes. # The input is FAST format files located in DATA.geno directory # The output is stored in OUT directory for CHR in {1..22} do time ./FAST \ --tped-file ./DATA.geno/chr$CHR.tped \ --snpinfo-file ./DATA.geno/chr$CHR.snp.info \ --mlinfo-file ./DATA.geno/chr$CHR.mlinfo \ --indiv-file ./DATA.geno/id.txt \ --out-file ./OUT/output\ --trait-file ./DATA.geno/Phenotype.tfam \ --gene-set ./DATA.geno/genes_list.txt \ --chr $CHR \ --mode genotype \ --linear-bf-perm \ --linear-minsnp-perm \ --linear-minsnp-gene-perm \ --linear-vegas-perm \ --linear-gwis-perm \ --linear-gates \ done
All methods using linear regression model, data format is IMPUTE2 output
#!/bin/bash # This script will run FAST in mode=genotype with linear model on all 22 chromosomes. # The input is IMPUTE2 format files located in DATA.geno directory # The output is stored in OUT directory for CHR in {1..22} do time ./FAST \ --impute2-geno-file ./DATA.geno/chr$CHR.impute2.geno \ --impute2-info-file ./DATA.geno/chr$CHR.impute2.info \ --indiv-file ./DATA.geno/id.txt \ --out-file ./OUT/output\ --trait-file ./DATA.geno/Phenotype.tfam \ --gene-set ./DATA.geno/genes_list.txt \ --chr $CHR \ --maf-cutoff 0.01 \ --mode genotype \ --max-perm 1000000 \ --linear-bf-perm \ --linear-minsnp-perm \ --linear-minsnp-gene-perm \ --linear-vegas-perm \ --linear-gwis-perm \ --linear-gates \ --flank 20000 \ --n-threads 1 done
All methods using logistic regression model
#!/bin/bash # This script will run FAST in mode=genotype with logistic model on all 22 chromosomes. # The input is FAST format files located in DATA.geno directory # The output is stored in OUT directory for CHR in {1..22} do time ./FAST \ --tped-file ./DATA.geno/chr$CHR.tped \ --snpinfo-file ./DATA.geno/chr$CHR.snp.info \ --mlinfo-file ./DATA.geno/chr$CHR.mlinfo \ --indiv-file ./DATA.geno/id.txt \ --out-file ./OUT/output\ --trait-file ./DATA.geno/Phenotype_binary.tfam \ --gene-set ./DATA.geno/genes_list.txt \ --chr $CHR \ --maf-cutoff 0.01 \ --mode genotype \ --max-perm 1000 \ --logistic-bf-perm \ --logistic-minsnp-perm \ --logistic-minsnp-gene-perm \ --logistic-vegas-perm \ --logistic-gwis-perm \ --logistic-gates \ --flank 20000 \ --n-threads 1 done
With New methods in FAST.2.4
Single SNP Cox-PH regression
#!/bin/bash # This script will run FAST in mode=genotype with single SNP Cox-PH model. # The input is from files in DATA.geno # The output is stored in OUT time ../FAST \ --impute2-geno-file ./DATA.geno/chr1.impute2.geno.gz \ --impute2-info-file ./DATA.geno/chr1.impute2.info.gz \ --indiv-file ./DATA.geno/id.txt.gz \ --out-file ./OUT/output.COX.impute2 \ --trait-file ./DATA.geno/Cox.Pheno \ --chr 1 \ --maf-cutoff 0.01 \ --mode genotype \ --cox-cov 3 \ --cox-strata 0 \ --cox-snp
Gene-based Cox-PH regression
#!/bin/bash # This script will run FAST in mode=genotype with gene-based Cox-PH model. # The input is from files in DATA.geno # The output is stored in OUT time ../FAST \ --impute2-geno-file ./DATA.geno/chr1.impute2.geno.gz \ --impute2-info-file ./DATA.geno/chr1.impute2.info.gz \ --indiv-file ./DATA.geno/id.txt.gz \ --out-file ./OUT/output.COX.impute2 \ --trait-file ./DATA.geno/Cox.Pheno \ --gene-set ./DATA.geno/genes1.txt.gz\ --chr 1 \ --maf-cutoff 0.01 \ --mode genotype \ --cox-cov 3 \ --cox-strata 0 \ --cox-gene\ --flank 0
SAPPHOI in genotype mode
#!/bin/bash # This script will run FAST in mode=genotype with SAPPHOI model. To run SAPPHOC, simply change the --SAPPHOI option to --SAPPHOC. # Format of the trait file please refer to the InputFile page # Have to specify --num-phenotypes, namely how many phenotypes SAPPHO is running on. # All other options, including the genotype inputs and run options, are exactly same as for single phenotype methods. time ../FAST \ --impute2-geno-file ./DATA.geno/chr1.impute2.geno.gz \ --impute2-info-file ./DATA.geno/chr1.impute2.info.gz \ --indiv-file ./DATA.geno/id.txt.gz \ --out-file ./OUT/output.PL.impute2 \ --trait-file ./DATA.geno/PL.Pheno \ --maf-cutoff 0.01 \ --mode genotype \ --num-phenotypes 4\ --sapphoI
SAPPHOI in summary mode
#!/bin/bash # This script will run FAST in mode=summary with SAPPHOI model. SAPPHOC could not be run in summary mode. # Format of the summary file please refer to the InputFile page # Have to specify --num-phenotypes, namely how many phenotypes SAPPHO is running on. # All other options, including the --ld-file, --allele-file, --hap-file, are exactly same as for single phenotype methods. time ../FAST \ --summary-file no example\ #Format of summary file please refer to InputFile page --ld-file ./DATA.summary/chr$CHR.ld\ --allele-file ./DATA.summary/chr$CHR.allele.info \ --pheno-varcov-file no example\ #Format of pheno-varcov-file please refer to InputFile page --out-file ./OUT/\ --maf-cutoff 0.01 \ --mode summary \ --num-phenotypes 4\ --sappho-alpha 0.2\ --sapphoI
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