| Option |
Parameter/default |
Description |
| Basic input/output |
--file | {plink} | Specify .ped and .map files |
--ped | {plink.ped} | Specify .ped file |
--map | {plink.map} | Specify .map file |
| | | |
--no-sex | | PED file does not contain column 5 (sex) |
--no-parents | | PED file does not contain columns 3,4 (parents) |
--no-fid | | PED file does not contain column 1 (family ID) |
--no-pheno | | PED file does not contain column 6 (phenotype) |
--liability | | PED file does contain liability (column 7) |
--map3 | | Specify 3-column MAP file format |
| | | |
--tfile | {plink} | Specify .tped and .tfam files |
--tped | {plink.tped} | Specify .tped file |
--tfam | {plink.tfam} | Specify .tfam file |
| | | |
--lfile | {plink} | Specify long-format: LGEN, FAM and MAP |
| | | |
--bfile | {plink} | Specify .bed, .bim and .fam |
--bed | {plink.bed} | Specify .bed file |
--bim | {plink.bim} | Specify .bim file |
--fam | {plink.fam} | Specify .fam file |
| | | |
--out | {plink} | Specify output root filename |
--silent | | Suppress output to console |
| | | |
--pheno | {phenofile} | Specify alternate phenotype |
--make-pheno | {file} {value} | Specify binary phenotype, with cases have value |
--make-pheno | {file} * | Specify binary phenotype, with cases are present |
--mpheno | {var #} | Specify which, if >1 phenotype column |
--pheno-name | {var name} | Instead of --mpheno, if a header row exists |
--all-pheno | | Perform association for all phenotypes in file |
--loop-assoc | {clusterfile} | Perform association for each level of cluster versis all others |
| | | |
--covar | {covarfile} | Specify covariate |
--mcovar | {var #} | Specify which, if >1 covariate column (for use with --gxe) |
--covar-name | {list} | Specify 1 or more covariates by name |
--covar-number | {list} | Specify 1 or more covariates by number |
| | | |
--within | {filename} | Specify clustering scheme |
--mwithin | {var #} | Specify which, if >1 cluster column |
| | | |
--script | {filename} | Include command-line options from file |
| | | |
| Selection of SNPs and
individuals |
--chr | {N} | Select a particular chromosome N |
--gene | {name} | Select a particular gene, given a SET file (--set) |
| | | |
--from | {SNP} | Select range from this SNP ... |
--to | {SNP} | ... to this SNP (must be on same chromosome) |
| | | |
--snps | {SNP list} | Select comma-delimited list of SNPs, allowing for ranges,
e.g. snp1,snp2,snp6-snp12
|
| | | |
--snp | {SNP} | Select this SNP ... |
--window | {kb} | ... and (optionally) all SNPs in the surrounding kb window |
| | | |
--from-bp | {bp} | Select SNPs within this window... |
--to-bp | {bp} | ... specified in base-pair position |
| | | |
--from-kb | {kb} | Select SNPs within this window... |
--to-kb | {kb} | ... specified in kilobases |
| | | |
--from-mb | {mb} | Select SNPs within this window... |
--to-mb | {mb} | ... specified in megabases |
| | | |
--extract | {snplist} | Extract list of SNPs |
--exclude | {snplist} | Exclude list of SNPs |
| | | |
--keep | {indlist} | Keep only these individuals |
--remove | {indlist} | Remove these individuals |
| | | |
--keep-before-remove | | Perform keep before remove (default opposite) |
--exclude-before-extract | | Perform exclude before extract (default opposite) |
| | | |
--filter | {filename} {value} | Filter individuals matching value |
--mfilter | {var #} | Specify filter value, if >1 filter column |
| | | |
--filter-cases | | Include only cases |
--filter-controls | | Include only controls |
--filter-males | | Include only males |
--filter-females | | Include only females |
--filter-founders | | Include only founders |
--filter-nonfounders | | Include only nonfounders |
--prune | | Remove individuals with missing phenotypes |
| | | |
| Other data management options |
--make-bed | | Make .bed, .fam and .bim |
--recode | | Output new .ped and .map files |
--recode12 | | As above, with 1/2 allele coding |
--recode-rlist | | List individuals with minor allele genotypes |
--recode-lgen | | Output data in long LGEN format |
| | | |
--recodeHV | | As above, with Haploview .info file |
--recode-fastphase | | Ouput fastphase format file |
--recode-bimbam | | Ouput bimbam format file |
--recode-structure | | Ouput structure format file |
| | | |
--recodeA | | Raw data file with additive coding |
--recodeAD | | Raw data file with additive/dominance coding |
--tab | | Delimit --recode and --recode12 with tabs |
--list | | Output one genotype per line, list of FIDs and IIDs |
--plist | {FID1 IID1 FID2 IID2} | Pairwise listing of genotypes for two individuals |
| | | |
--write-snplist | | List only the (filtered) SNPs in the dataset |
--update-map | {filename} | Update physical positions in a map file |
--update-cm | | Update genetic distances in a map file |
--update-name | | Update SNP names in a map file |
--update-chr | | Update chromosome codes in a map file |
| | | |
--update-ids | {file} | Update FIDs and IIDs in a file |
--update-sex | {file} | Update sex information in a file |
--update-parents | {file} | Update parent codes in a file |
| | | |
--write-covar | | Output ordered, filtered covariate file |
--with-phenotype | | Include PED/phenotype information in new covariate file |
--dummy-coding | | Downcode categorical covariates to binary dummy variables |
| | | |
--merge | {pedfile}, {mapfile} | Merge in a PED/MAP fileset |
--bmerge | {bedfile}, {bimfile}, {famfile} | Merge in a binary fileset |
--merge-list | {list file} | Merge multiple standard and/or binary filesets |
--merge-mode | {1} | Specify merge mode (1-7) |
| | | |
--zero-cluster | {filename} | Zero-out specific SNPs for specific clusters |
--oblig-missing | {filename} | SNPs/clusters that are obligatory missing |
--oblig-cluster | {filename} | Individuals/clusters defining obligatory missingness |
| | | |
--flip | {snplist} | Flip strand of SNPs in list |
--flip-subset | {individual-list} | Flip strand of SNPs only for these individuals in list |
--flip-scan | | LD-based heuristic to look for SNPs flipped between cases and controls |
| | | |
--1 | | 0/1 unaffected/affected coding |
--compound-genotypes | | Use AA, AG, 00 coding (no spaces between alleles in PED file) |
--missing-phenotype | {-9} | Missing phenotype code |
--missing-genotype | {0} | Missing genotype code |
--output-missing-phenotype | {-9} | Missing phenotype code for output |
--output-missing-genotype | {0} | Missing genotype code for output |
--allele1234 | | Convert (A,C,G,T) to (1,2,3,4) |
--alleleACGT | | Convert (1,2,3,4) to (A,C,G,T) |
--update-alleles | {file} | Update allele codes in a file |
--reference-allele | {file} | Force a particular reference (A1) allele |
--keep-allele-order | | Do not flip A1 to be the minor allele |
| | | |
--allow-no-sex | | Do not set ambiguously-sexed individuals missing |
--must-have-sex | | When making a new dataset, do set ambiguously-sexed individuals missing |
--set-hh-missing | | Making new fileset, set heterozygous haploids missing |
--set-me-missing | | Making new fileset, set Mendel errors missing |
| | | |
--make-founders | | Set non-founders without two parents to founders |
--pedigree | | When performing TDT, dump parsed family structure |
--tucc | | Make pseudo case/control pairs form trio data |
| | | |
| Reporting summary statistics |
--freq | | Allele frequencies |
--counts | | Modifies --freq to report actual allele counts |
--nonfounders | | Include all individuals in MAF/HWE calculations |
| | | |
--missing | | Missing rates (per individual, per SNP) |
--test-missing | | Test of missingness differing by case/control status
| --test-mishap | | Haplotype-based test for non-random missingness |
--cluster-missing | | IBM clustering |
| | | |
--hardy | | Report Hardy-Weinberg disequilibrium tests (exact) |
--hardy2 | | Report Hardy-Weinberg disequilibrium tests (asymptotic) |
--mendel | | Report Mendel error checks |
| | | |
--check-sex | | Use X chromosome data to check an individual's assigned sex |
--impute-sex | | Use X chromosome data to impute an individual's assigned sex |
| | | |
--within | {cluster file} | Stratify frequencies and missing rates by clusters |
| | | |
| Inclusion thresholds |
--maf | {0.01} | Minor allele frequency |
--max-maf | {1} | Maximum minor allele frequency |
--geno | {0.1} | Maximum per-SNP missing |
--mind | {0.1} | Maximum per-person missing |
--hwe | {0.001} | Hardy-Weinberg disequilibrium p-value (exact) |
--hwe2 | {0.001} | Hardy-Weinberg disequilibrium p-value (asymptotic) |
--hwe-all | | HW filtering based on all founder individuals for binary trait
(instead of just unaffecteds) |
--me | {0.1} {0.1} | Mendel error rate thresholds (per SNP, per family) |
--cell | {5} | Minimum genotype cell count for --model |
--min | {0} | Minimum pi-hat
for --genome output |
--max | {1} | Maximum pi-hat for --genome output |
| | | |
| Quality scores |
--qual-scores | {file} | SNP based quality scores filter |
--qual-threshold | {0.8} | SNP quality score threshold |
--qual-max-threshold | {1} | SNP maximum quality scores threshold |
--qual-geno-scores | {file} | Genotype-based quality scores filter |
--qual-geno-threshold | {0.8} | Genotype quality score threshold |
--qual-geno-max-threshold | {1} | Genotype maximum quality scores threshold |
| | | |
| IBS stratification / clustering |
--genome | | Calculate IBS distances between all individuals |
--cluster | | Perform clustering |
--matrix | | Output IBS (similarity) matrix |
--distance-matrix | | Output 1-IBS (distance) matrix |
--mc | {0} | Maximum cluster size |
--cc | | Cluster by phenotype |
--mcc | {0 0} | Maximum number of cases/controls per cluster |
--ibm | {0.01} | Constrain IBS matching on IBM matching |
--ppc | {0.01} | IBS test p-value threshold (was --pmerge) |
--ppc-gap | {500kb} | Skip SNPs within this for PPC test |
--match | {match-file} | Specify external categorical matching criteria |
--match-type | {match-type-file} | Specify external categorical matching direction (+/- match) |
--qmatch | {match-file} | Specify external quantitative matching criteria |
--qt | {threshold-file} | Specify quantitative matching thresholds |
--neighbour | {N} {M} | Outlier statistics (for nearest neighbours N to M) |
| | | |
| Whole genome summary statistics |
--genome | | Output genome-wide IBS/IBD |
--rel-check | | Only calculate IBS/IBD for members of same family (FID) |
--read-genome | {genome-file} | Read previously-computed genome values |
--nudge | | Adjusted estimated IBD values |
--impossible | | Indicate 'impossible' estimated IBD values |
--het | | Individual inbreeding F / heterozygosity |
--homozyg-kb | {kb} | Identify runs of homozygosity (kb) |
--homozyg-snp | {N SNPs} | Identify runs of homozygosity (# SNPs) |
--homozyg-het | {N hets} | Allow for N hets in run of homozygosity |
--homozyg-group | | Group pools of overlapping segments |
--homozyg-match | {0.95} | Identity threshold for allelic matching overlapping segments |
--homozyg-verbose | | Display actual genotypes for each pool |
| | | |
| Association analysis procedures |
--assoc | | Case/control or QTL association |
--fisher | | Fisher's exact (allelic) test |
--model | | Cochran-Armitage and full-model C/C association |
--model --fisher | | Exact full-model tests |
| | | |
--T2 | | Hotelling's T(2) multilocus test |
| | | |
--mh | | Cochran-Mantel-Haenszel SNPxDISEASE|STRATA |
--mh2 | | Cochran-Mantel-Haenszel SNPxSTRATA|DISEASE |
--bd | | Breslow-Day homogeneity of odds ratios test |
--homog | | Partitioning chi-square homogeneity of odds ratios test |
| | | |
--gxe | | QTL interaction test (dichotomous covariate only) |
| | | |
--linear | | Test for quantitative traits and multiple covariates |
--logistic | | Test for disease traits and multiple covariates |
--genotypic | | Include dominance term in model, and 2df model |
--dominant | | Fit dominant model for minor allele |
--recessive | | Fit recessive model for minor allele |
--condition | {SNP} | Include additive effect of SNP in model |
--condition-list | {filename} | Include additive effects of these SNPs in model |
--sex | | Include sex effect in model |
--interaction | | Include SNP x covariate interactions |
--test-all | | Joint test of all terms in model |
--parameters | {1,2,...} | Fit only a subset of model terms |
| --tests | {1,2,...} | Joint test of user-specified set of parameters |
--beta | | Make --logistic return coefficients, not odds ratios |
| | | |
--tdt | | Family-based TDT and parenTDT (permute TDT) |
--parentdt1 | | As above, except permuted statistic is parental test |
--parentdt2 | | As above, except permuted statistic is combined test |
--poo | | Parent-of-origin analysis in TDT |
| | | |
--dfam | | Disease family-test (families and
unrelateds) |
| | | |
--ci | {0.95} | Confidence interval for CMH odds ratios |
| | | |
--set-test | | Set-based association (requires --mperm) |
--set-p | {p-value} | p-value threshold for set-based test |
--set-r2 | {r^2} | R-squared threshold for set-based test |
--set-max | {N SNPs} | Maximum number of SNPs in set |
| | | |
| Permutation procedure options |
--perm | | Run permutations (adaptive-mode) |
--mperm | {1000} | # of permutations in max-perm mode |
--aperm | {...} | Parameters (six) for adaptive permutation mode |
--rank | | Modifies --mperm for rank-based permutation |
| | | |
--model-trend | | Use CA-trend test from --model |
--model-gen | | Use genotypic test from --model |
--model-dom | | Use dominant test from --model |
--model-rec | | Use recessive test from --model |
| | | |
--genedrop | | Permutation by gene-dropping simulation (family-data) |
--swap-parents | | Labal-swap permutation for parents when gene-dropping |
--swap-sibs | | Labal-swap permutation for siblings when gene-dropping |
--swap-unrel | | Labal-swap permutation for unrelateds when gene-dropping |
| | | |
--family | | Make Family ID the cluster |
| | | |
--p2 | | Alternate permutation scheme (C/C only) |
| | | |
| Epistasis analysis |
--epistasis | | Perform SNP x SNP epistatic analysis |
--fast-epistasis | | Quick SNP x SNP screening for C/C data |
--twolocus | {SNP} {SNP} | Display contingency table for two SNPs |
--case-only | | Case-only epistatic analysis |
--gap | {1000} | Gap (kb) for SNP x SNP case-only epistasis tests |
--epi1 | {0.0001} | Output p-value threshold: pairs |
--set-by-all | | Test set 1 SNPs paired with all others |
--nop | | Do not calculate p-values (fast screening) |
| | | |
--genepi | | Gene-based test for epistasis |
| | | |
| Haplotype inference and linkage disequilibrium |
--hap-snps | {snplist} | Specify a list of SNPs to phase |
--hap-window | {N} | Specify haplotype sliding window |
--hap | {tagfilename} | Multimarker predictor / haplotype list |
--whap | {tagfilename} | Weighted haplotype test list |
| | | |
--hap-assoc | | Perform haplotype-based case/control association |
--hap-tdt | | Perform haplotype-based TDT |
--hap-freq | | Output haplotype frequencies for entire sample |
--hap-phase | | Output individual haplotype phases |
--hap-phase-wide | | Output individual haplotype phases, wide-format |
| | | |
| | | |
--hap-impute | | Create fileset with imputed haplotypes as SNPs |
--hap-pp | {0.8} | Posterior probability threshold |
--hap-miss | {0.5} | Proportion of missing genotypes allowed |
--hap-min-phase-prob | {0.01} | Minimum reported phase probability |
--hap-max-phase | {N} | Maximum number of phases considered per person |
--mhf | {0.01} | Minor haplotype frequency threshold |
| | | |
| Proxy association and imputation methods |
--proxy-assoc | {SNP/all} | Proxy association methods |
--proxy-glm | | Use linear models in proxy association |
--proxy-drop | | Drop then re-impute observed genotypes |
--proxy-tdt | {SNP/all} | Proxy TDT association methods |
| | | |
--proxy-impute | {SNP/all} | Proxy imputation methods |
--proxy-replace | | Replace observed genotypes |
--proxy-dosage | | Also output dosage file |
--proxy-impute-threshold | {0.95} | Per-genotype threshold to impute for an individual |
| | | |
--proxy-list | {file} | Specify SNPs to impute/test |
--proxy-flanking | {file} | Specify proxies for single reference SNP |
| | | |
--proxy-r2 | {0 0.05 0.5} | Proxy selection LD parameters |
--proxy-maxsnp | {5} | Maximum number of proxies tto select |
--proxy-window | {15} | Proxy SNP search space (SNPs) |
--proxy-kb | {250} | Proxy SNP search space (kb) |
| | | |
--proxy-b-threshold | {0.1} | MAF threshold for rare alleles (plan B) |
--proxy-b-r2 | {0 0.05 0.5} | Alternate proxy selection LD parameters |
--proxy-b-maxsnp | {0.1} | Alternate maximum number of proxies to use |
--proxy-b-window | {0.1} | Alternate proxy SNP search space (SNPs) |
--proxy-b-kb | {250} | Alternate proxy SNP search space (kb) |
| | | |
--proxy-maf | {0.01} | Proxy SNP MAF threshold |
--proxy-geno | {0.05} | Proxy SNP missingness threshold |
--proxy-r2-no-filter | | No LD-based proxy selection |
| | | |
--proxy-mhf | {0.05} | Proxy haplotype frequency threshold |
--proxy-sub-r2 | {0.8} | Minimum r-squared with reference for haplotypic proxies (verbose mode) |
--proxy-sub-maxsnp | {3} | Maximum number of SNPs per haplotypic proxy (verbose mode) |
| | | |
--proxy-verbose | | Verbose mode |
--proxy-show-proxies | | List actual proxies in non-verbose mode |
--proxy-genotypic-concordance | | In imputation, show genotypic-specific concordance |
| | | |
| Conditional haplotype association tests |
--chap | | Main conditional-haplotype test command |
--specific-haplotype | {haplotype(s)} | Test for specific haplogroup effect |
--independent-effect | {snp{s}} | Test for independent effect |
--control | {snp(s)/haplotype(s)} | Control for certain effects |
| | | |
--alt-snp | | Specify SNP groupings under alternate |
--null-snp | | Specify SNP groupings under null |
| | | |
--alt-group | | Specify haplogroupings under alternate |
--null-group | | Specify haplogroupings under null |
| | | |
--test-snp | | Drop 1 or more conditioning SNPs |
--each-versus-others | | Each all haplogroup-specific p-values |
--each-vs-others | | As above |
| | | |
| LD-based result clumping |
--clump | {file(s)} | Comma-delimited result files |
--clump-p1 | {1e-4} | p-value threshold for index SNPs |
--clump-p2 | {1e-2} | p-value threshold for clumped SNPs |
--clump-r2 | {0.2} | r^2 (LD) threshold for clumping |
--clump-kb | {250} | kb-threshold for clumping |
| | | |
--clump-replicate | | Only report multi-file clumps |
--clump-best | | For each SNP in the first file, find the best proxy from the other files |
--clump-verbose | | Specifty verbose output |
--clump-range | {filename} | Add gene/region range information to clumped output |
--clump-range-border | {kb} | Use a kb border around each gene/region |
--clump-annotate | {field(s)} | Include these fields in verbose mode |
--clump-field | {field} | Specifty p-value field other than P |
--clump-index-first | | Only index based on first results file |
--clump-allow-overlap | | Specify that a SNP can appear in more than one clump |
| | | |
| Annotation and meta-analysis of results |
--annotate | {filename} | Annotate result file |
| | | |
--meta-analysis | {filenames} | Meta-analysis of multiple result files |
| | | |
--gene-report | {filename} | Results file to perform gene-report on |
--gene-list | {filename} | List of genes/regions for reporting |
--gene-list-border | {kb} | Add a kb border aroud each gene/region |
--gene-subset | {filename} | Only report on a subset of genes, listed here |
--gene-report-empty | | Report genes without any informative SNPs |
| | | |
| LD pruning and pairwise LD |
--indep | {N M VIF} | VIF pruning (N-SNP window, shifted at M-SNP intervals) |
--indep-pairwise | {N M r^2} | r^2 pruning (as above) |
--r | | Pairwise SNPxSNP LD (r) |
--r2 | | Pairwise SNPxSNP LD (r^2) |
--ld-window | {N} | Limit pairwise SNPxSNP to within a N SNP window |
| | | |
| Definition of SETs |
--set | {setfilename} | SET definitions |
--subset | {filename} | Only read of subset of SETs from --set |
--set-table | | Output a SNP by SET matrix |
| | | |
| Copy number variants (CNV) analysis |
--gfile | {fileset} | Load generic variant file |
--cfile | {fileset} | Load segmental CNV fileset (CNV, FAM, MAP) |
--cnv-list | {filename} | Load segmental CNV list |
| | | |
--cnv-del | | Filter only deletions |
--cnv-dup | | Filter only duplications |
| | | |
--cnv-intersect | {filename} | Include segments intersecting with regions |
--cnv-exclude | {filename} | Exclude segments intersecting with regions |
--cnv-disrupt | | Include/Exclude segments that start or stop within a gene/region |
--cnv-count | {filename} | Count number of regions intersected by CNVs |
--cnv-border | {kb} | Add a kb border around each region |
| | | |
--cnv-freq-excldue-above | N | Exclude CNVs overlapping regions with more than N CNVs |
--cnv-freq-excldue-below | N | Exclude CNVs overlapping regions with fewer than N CNVs |
--cnv-freq-excldue-exact | N | Exclude CNVs overlapping regions with exactly N CNVs |
--cnv-freq-incldue-exact | N | Include CNVs overlapping regions with exactly N CNVs |
--cnv-freq-method2 | | Use alternative method for determining CNV frequency |
| | | |
--cnv-overlap | {N} | Define overlap of CNV and region by CNV length |
--cnv-union-overlap | {N} | Define overlap of CNV and region by union |
--cnv-region-overlap | {N} | Define overlap of CNV and region by region length |
| | | |
--cnv-write | | Create a new CNV and FAM file |
--cnv-write-freq | | Include frequency counts if --cnv-freq-method2 specified |
--cnv-make-map | | Create a new MAP file from a CNV and FAM file |
--cnv-report-regions | | List regions that are intersected by CNVs |
--cnv-verbose-report-regions | | Verbose listing of regions that are intersected by CNVs |
--cnv-subset | {filename} | Define overlap of CNV and region by region length |
| | | |
--cnv-track | {kb} | Create a UCSC-compatible BED track for viewing CNVs |
--cnv-blue | {kb} | Make this CNV track blue |
--cnv-red | {kb} | Make this CNV track red |
--cnv-green | {kb} | Make this CNV track green |
--cnv-brown | {kb} | Make this CNV track brown |
| | | |
--cnv-kb | {N} | Exclude segments below N kb |
--cnv-max-kb | {N} | Exclude segments above N kb |
--cnv-score | {N} | Exclude segments below N score |
--cnv-max-score | {N} | Exclude segments above N score |
| | | |
--cnv-drop-no-segment | | Remove individuals with no segments |
--cnv-unique | | Exclude CNVs seen in both cases and controls |
--cnv-seglist | {kb} | Create a printout of CNVs |
| | | |
--cnv-indiv-perm | | Permutation test for genome-wide CNV burden |
--cnv-test-2sided | | Use 2-sided approach for empirical p-values |
--cnv-test-window | {kb} | Extend test to a region extending kb distance on either side of position |
--cnv-test-region | {kb} | Test regions for CNV case/control differences |
| | | |
| Data simulation options |
--simulate | {filename} | Simulate SNP population-based data |
--simulate-ncases | {100} | Number of cases to simulate |
--simulate-ncontrols | {100} | Number of controls to simulate |
--simulate-prevalence | {0.01} | Disease prevalence in population |
--simulate-qt | {filename} | Simulate quantitative trait dataset |
--simulate-label | {label} | Add identifier label to simulated individuals |
--simulate-tags | | Simulate tags instead of causal variants |
--simulate-haps | | Simulate causal variant / tag SNP pairs |
| | | |
--dummy | {N} {M} | Generate dataset of N individuals on M SNPs |
| | | |
| Misc analysis output options |
--adjust | | Output adjusted p-values and calculate genomic control |
--lambda | {X} | Set lambda to X instead of estimating from data |
--qq-plot | | Generate entries to faciliate a Q-Q plot in adjusted output |
| | | |
| Misc. |
--help | | Display list of options |
--dog | | Set chromosome codes for dog |
--mouse | | Set chromosome codes for mouse |
--horse | | Set chromosome codes for horse |
--cow | | Set chromosome codes for cow |
--sheep | | Set chromosome codes for sheep |
| | | |
--lookup | {SNP rs#} | Lookup WGAS SNP annotation information |
--lookup-gene | {gene name} | List all SNPs in gene |
--lookup-list | {snplist filename} | SNP annotation for multiple
SNPs |