• Input/Output/Program flow

• InfoQC analysis

• Trait analysis

• Linkage analysis

• Association analysis

• Epistasis analysis

• Data management

Name	Description
Default input file
--fam <path>	Specify the name of PLINK format family file(.fam).
--vcf <path>	Specify the name of Variant Calling Format file (.vcf).
Optional/alternative input file
--bed <path>	Specify the name of PLINK binary format .bed file.
--bim <path>	Specify the name of PLINK binary format .bim file.
--pheno <path>	Specify the name of phenotype file, space delimited, with header line, the first 5 columns to be named as (FID IID fatid matid sex) and contains the same information as in .fam file, the phenotype data starting from 6th column.
--set <path>	Specify the name of geneset file for gene-based association analysis, see the gene-based association analysis section for detail.
--par	Specify the name of parameter file for segregation analysis, see the segregation analysis section for detail.
--typ	Specify the name of type probability file for model-based linkage analysis (LODLINK), see the model-based linkage analysis section for detail.
--map <path>	Specify the name of map file for model-free linkage analysis (MERLIN), see the model-free linkage analysis section for detail.
--script <path>	Specify the name of script file including all command-line options selected for a run.
Output file
--out <path_prefix>	Specify the root name of output file(s) for a run
Input data handling
--1sex	Sex is coded as (0=male; 1=female; other=unknown), the deafult is (1=male; 2=female; other=unknown).
--1case	Case/control status is coded as (0=control; 1=case; other=unknown) for binary trait, the deafult is (1=control; 2=case; -9=missing).
--mispheno <string>	Specify the missing value for phenotype in fam file when other than -9 is used.
--misgeno <string>	Specify the missing value for genotype in vcf file when other than 0 or NA is used.
--model <additive|dominant>	Specify the genetic model (additive or dominant) to use.
Other
--pname <string[(,string)+]>	Specify the name of main trait(s) for a run, use with --pheno option.
--cname <string[(,string)+]>	Specify the name of covariate(s) for a run, use with --pheno option.
--thread <integer>	Specify the number of threads to be used for a run.
--verbose	Report the additional analyses information.

Name	Description
Variant information
--fst	Compute Fst, need to specify a column name from pheno file for group information.
--tstv	Compute Ts/Tv ratio, need to specify a positive number.
--freq	Compute the allele frequences.
--hwe	Perform Hardy-Weinburg Eqilibrium test.
--pca	Compute the principal components.
--npc	Specify the number of principal components to compute, use with --pca option.
Sample information
--het	Find the heterozygote.
--hethom	Find the heterozygote/homozygote ratio.
Pedigree information
--famuniq	Export SNV list of uniquely exists in the specific famliy.
--relpair	Find all relative pairs in pedigree data.
--plot	Plot pedigree(s).
Error detection
--mendel	Check for medelian error(s).
Relatedness
--makecor	Compute the relationship matrix using GRM matrix by default.
--kinship	Use kinship matrix instead of GRM, use with --makecor (and all analyses that use the relationship matrix).
--ibs	Use ibs matrix instead of GRM, use with --makecor (and all analyses that use the relationship matrix).

Name	Description
Familial aggregation
--fcor	Compute multivariate familial correlations with their asymptotic standard errors.
--fcorStdErrOff	Do not calculate the asymptotic standard errors, axillary option of --fcor option.
Heritability
--heritability	Compute narrow-sense heritability i.e., the proportion of phenotypic variation due to additive genetic values, using GRM, kinship or IBS matrix.
Segregation analysis
--segreg	Perfom comingling analysis (by default) or segregation analysis (when a parameter file is given with --par option).

Name	Description
Model-based, two-point
--lodlink	Compute LOD score and recombination fraction between a marker and trait and perform linkage test.
--lodlinkLinkageTestOff	Do not perform linkage test, use with --lodlink option.
--lodlinkLinkageHomogOff	Perform linkage test not assuming linkage homogeneity, use with --lodlink option.
--lodlinkLinkageSexSpecific	Perform linkage test using sex-specific recombination fraction, use with --lodlink option.
--lodlinkSmithHomogTest	Perform Smith's test for linkage homogeneity, use with --lodlink option.
Model-free, multipoint
--merlin	Compute Zscore, p-value assuming normal approximation, Kong and Cox delta, K&C LOD score and K&C p-value.

Name	Description
Single variant
--regression	Perform regression test.
--scoretest	Perform score test.
--tdt	Perform transmission/disequilibrium test.
--sdt	Perform sib transmission/disequilibrium test.
--mqls	Perform more powerful quasi-likelihood score (MQLS) test.
--fqls	Perform an extended MQLS test for ascertained families.
--prevalence	Specify the prevalence value to be used in the analysis, use with --fqls option.
--heri	Specify the heritability value to be used in the analysis, use with --fqls option.
--gemma	Perform linear mixed model test.
--multifqls	Perform an extended MQLS test for multiple traits.
Gene-based (related/family samples)
--genesummary	Generate gene-wise summary.
--genetest	Perform test by combined multivariate and collapsing (CMC) method.
--pedcmc	Perform test by an extended CMC method for family data, use with --genetest option.
--famvt	Perform test by an extended variable threshold method for family data, use with --genetest option.
--skat	Perform SNP-set (sequence) kernel association test (SKAT), use with --genetest option.
--skato	Perform an extension of SKAT, optimal SKAT, use with --genetest option.
--farvat	Perform a family-based rare variant association test (FARVAT), an extended MQLS test for rare variants, use with --genetest option.
--pedgene	Perform test by collapsing and kernel methods, use with --genetest option.
--farvatx	Perform an extended FARVAT for X chromosome, use with --genetest option.
--mfarvat	Perform an extended FARVAT for multiple traits, use with --genetest option.
--fbskat	Perform FB-SKAT for binary trait.
--rvtdt	Perform rv-TDT for binary trait.
Gene-based (unrelated/independent samples)
--genesummary	Generate gene-wise summary.
--genetest --indep	Perform test by combined multivariate and collapsing (CMC) method.
--vt --indep	Perform test by an variable threshold, use with --genetest option.
--skat --indep	Perform SNP-set (sequence) kernel association test (SKAT), use with --genetest option.
--skato --indep	Perform an extension of SKAT, optimal SKAT, use with --genetest option.
--kbac --indep	Perform test by the kernel-based adaptive cluster method, use with --genetest option.

Name	Description
MDR-related options
--order <integer>	Set order of combinations to investigate SNP-SNP interaction. In default, only the first order will be investigated.
--measure <string>	Set a measure to sort the results. This option will affect only if --top is assigned.In default, Balanced Accuracy (ba) will be used. Currently available parameters are: ba.
--top <integer>	Reports only top K results with largest measure (BA in default). Without this option, all combinations will be reported.
MDR analyses
--mdr	Perform Multidimensional Dimensionality Reduction (MDR) analysis to investigate SNP-SNP interactions. This option is only applicable to binary phenotype.
--gmdr	Perform Generalized MDR analysis. Unlike MDR, this analysis can be applied to both binary and continuous phenotype, and is able to adjust covariates.
--cname <string[(,string)+]>	Specify the name of covariate(s) for a run, use with --pheno option.

Name	Description
VCF specific filterings
--filqual <integer>	Exclude variants from the analysis when its QUAL field value is within the given criteria.
--incqual <integer>	Include variants to the analysis when its QUAL field value is within the given criteria.
--vcfqc	Include variants to the analysis when its FILTER field value is PASS.
--phasedonly	Include only phased genotypes to the analysis.
--unphasedonly	Include only unphased genotypes to the analysis.
Variant filterings
--remvariant <list_or_path>	Exclude matching variants from the analysis.
--selvariant <list_or_path>	Include matching variants to the analysis.
--filmaf <range>	Exclude variants from the analysis when its Minor Allele Frequency (MAF) is within the given criteria.
--incmaf <range>	Include variants to the analysis when its Minor Allele Frequency (MAF) is within the given criteria.
--filmac <range>	Exclude variants from the analysis when its Minor Allele Count (MAC) is within the given criteria.
--incmac <range>	Include variants to the analysis when its Minor Allele Count (MAC) is within the given criteria.
--filgvar <range>	Exclude variants from the analysis when its genotype calling rate is within the given criteria.
--incgvar <range>	Include variants to the analysis when its genotype calling rate is within the given criteria.
--filhwe <range>	Exclude variants from the analysis when its p-value of Hardy-Weinberg Equilibrium (HWE) test is within the given criteria.
--inchwe <range>	Include variants to the analysis when its p-value of Hardy-Weinberg Equilibrium (HWE) test is within the given criteria.
--filmendelvar <range>	Exclude variants from the analysis if overall Mendelian error rate of a variant within the given condition.
--incmendelvar <range>	Include variants from the analysis if overall Mendelian error rate of a variant within the given condition.
--incmistest <range>	Include variants to the analysis when its p-value of missingness test is within the given range.
--filmistest <range>	Exclude variants from the analysis when its p-value of missingness test is within the given range.
--filrange	Exclude variants from the analysis when its physical position is within the given range.
--incrange	Include variants to the analysis when its physical position is within the given range.
--autoonly	Include only autosomal variants to the analysis.
--sexonly	Include only sex-chromosome variants to the analysis.
--chr	Include variants on the specified chromosomes to the analysis.
--snvonly	Include only Single Nucleotide Variants (SNVs) to the analysis.
--indelonly	Include only insertions and deletions to the analysis.
Sample filterings
--remsamp <list_or_path>	Exclude matching samples from the analysis.
--selsamp <list_or_path>	Include matching samples to the analysis.
--remfam <list_or_path>	Exclude matching families from the analysis.
--selfam <list_or_path>	Include matching families to the analysis.
--filgind <range>	Exclude samples from the analysis when its genotype calling rate is within the given criteria.
--incgind <range>	Include samples to the analysis when its genotype calling rate is within the given criteria.
--filmispheno	Exclude samples from the analysis when its primary phenotype is missing.
--filcase	Exclude samples from the analysis when its primary phenotype is binary and its response is case(or affected).
--filcontrol	Exclude samples from the analysis when its primary phenotype is binary and its response is control(or unaffected).
--filmendelfam <range>	Exclude all samples in the specific family from the analysis if overall Mendelian error rate of a family within the given condition.
--incmendelfam <range>	Include all samples in the specific family from the analysis if overall Mendelian error rate of a family within the given condition.
--filmendelsamp <range>	Exclude samples from the analysis if overall Mendelian error rate of a sample within the given condition.
--incmendelsamp <range>	Include samples from the analysis if overall Mendelian error rate of a sample within the given condition.
--sampresize <0~1>	Randomly resize the number of samples into the given proportion.
--sampresize <integer>	Randomly resize the number of samples into the given number.
--filmale	Exclude samples from the analysis when its gender is male.
--filfemale	Exclude samples from the analysis when its gender is female.
--filnosex	Exclude samples from the analysis when its gender is unknown(not male nor female).
--filmf	Filtering out "missing founders". When a sample is nonfounder but both parents are lacked in the dataset, both parents are regarded as "missing founders" and the sample will be treated as founder with --filmf.
--filnf	Exclude all nonfounders from the analysis.
--incsample <expression>	Include samples to the analysis when the given conditions are satisfied.
--filmispheno <expression>	Exclude samples from the analysis when the given conditions are satisfied.
LD-based prunings
--prunevif <window_size>,<step_size>,<vif_threshold>	Perform VIF-based LD pruning for VIF > <vif_threshold>, with <window_size> by stepping <step_size> variants
--prunepw <window_size>,<step_size>,<r2_threshold>	Perform pairwise r^2-based LD pruning for r^2 > <r2_threshold>, with <window_size> by stepping <step_size> variants