| Global Commands |
|---|
| !|# | comment
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| echo | print text
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| $ <cmd> | shell command
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| dir <args> | file listing for current directory
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| pwd <dir> | print or change current directory
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| file del | ren | cat | que <fil> [<fil>] | delete | rename | cat | test file(s)
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| file vcf <fil> (<sta> <fin>)|<loc>... | summarize VCF file
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| file tbi <fil> [<pos>|<loc> [ann]] | summarize tabix index file or find record
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| file fas <fil> (<sta> <fin>)|index | summarize or index FASTA file
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| file print [/<str>/] [(<fmt>)] [+] [NR] [<col1>...<colN>] ;<fil> | print/search a file
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| file tra | inv <fil> [<fil>] | transpose | invert file(s)
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| file met <fil> | Fisher combine (meta-analyse) P-values in file
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| show annotation <vcf> [<var>...<varN>] | show or tabulate VCF file INFO variable values
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| clear [data] | reset
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| help [<key> | Al | Gl | Op | Da | An] | help
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| info | program information
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| list | ls [<loc1> [[to <locN> [$(a | q | m | h | x) [m | r]] | list loci
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| list where position [<chr:pos> [-- <chr:pos>] | list loci by map position/range
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| list where <string> | list loci where annotation matches search string
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| which [<loc1> [[to <locN> [$(a | q | m | h | x) [m | r]] | list positions of loci
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| show loci | locus information
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| show spectra | Tabulate loci by allelic spectrum
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| show pedigrees | tabulate pedigrees
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| show ids | tabulate IDs
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| show chromosome | current chromosomes
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| show map | show linkage map
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| show macros | list macros
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| show missing | count missing data for each locus
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| time | total elapsed time
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| set timer | time procedures
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| include [<fil>] | read commands from file
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| output [<fil>] | divert text output to a file
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| last [<num>] | command history
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| quit | exit program
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| set prompt | display prompt
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| set gui on | off | activate GUI
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| set ndecimal_width | output decimal digits
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| set epoch [jul | iso | mjd | <epo>] | set epoch for Julian dates
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| set out | ple -1 | 0 | 1 | 2 | ver | on | off | output verbosity
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| set printstyle rec | pai | obs | ver | <mask> | output style for print command
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| set tab <sep> | column separator for summary tables
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| set genotype_separator <sep> | allele separator for writing genotypes
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| set mis <str> | set missing data token for printing
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| set weight founders | Weighted allele frequency estimator
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| set analysis [imp | obs] | Include imputed alleles in regression
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| set burn-in <it> | No. of MCMC burn-in iterations
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| set iteration <it> | Max MC iterations
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| set emit <it> | No. of EM iteration
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| set jack <it> | size of jackknife draw
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| set batch <num> | No. of MCMC batches
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| set chain <num> | No. of MCMC chains
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| set tune <tun> | MCMC tuning parameter
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| set tolerance [<abs> ] | Maximizer convergence criterion
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| set mft <num> [<abs> [<rel>]] | MFT evaluation count and tolerance
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| set mincount <num> | Min MC iterations
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| set seeds <s1> <s2> <s3> | RNG seeds
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| set fbatimpute on | off | FBAT imputation
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| set sml <pA> <penAA> <penAB> <penBB> | default SML model
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| set tdt | TDT family selection
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| set ibd [<cM> [<Nmark>]] | Threshold for lumping markers for multipoint ibd
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| set model allelic | genotypic | allelic or genotypic marker encoding for regression model
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| set hre zero | chi | assume zero recomb for phased LD model
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| set nhap <maxhap> | maximum number of haplotypes for full log-linear LD model
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| set map function kosambi | haldane | linkage mapping function |
| Utilities
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|---|
| pchisq <x2> <df> [(ncp <df2>) | <df2>] | Chi-square or F-dist
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| qchisq <pvalue> <df> | Chi-square quantiles
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| power [[ncp] <ncp>] [n <nobs>] [p <pval>] [df <df>] | LRT power
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| chisq <nr> <nc> | Contingency Chi-square
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| polychoric <nr> <nc> | Polychoric correlation for contingency table
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| proportion <num> <den> [<width>] | CI for proportion
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| tetrachoric <prev> <rec risk ratio> | tetrachoric correlation
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| sml <pA> <penAA> <penAB> <penBB> | recurrence risks
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| grr <prev> <pA> <GRR> [<add | dom | rec>] | recurrence risks
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| grr <prev> <pCa> <pCo> case-control | recurrence risks
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| ito <pA> [<penAA> <penAB> <penBB>] | carrier rates in relatives
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| Basic Language Objects
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| 0,1,0.23 | Numbers
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| pi y n x | Named constants
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| "1" "a" "is a string" | Quoted strings
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| "<all>/<all>" | Genotypes
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| Alleles are 1..999, A-Z, a-z
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| Operators
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| ( ) ; : | Grouping and precedence
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| : | Separate sequence of expressions
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| * | / | + | - | ^ | Arithmetic
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| < | > | =< | => | ge | le | eq | == | ne | ^= | and | or | Comparison
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| if | then | Conditional statement execution
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| Mathematical Functions
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| log | sqrt | exp | sin | cos | tan | asin | acos | atan | abs | Maths functions
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| pnorm | qnorm | Statistical functions
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| int | round | Truncating functions
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| rand | rnorm | Uniform or Gaussian random numbers
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| greg | julian | Date functions
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| Data Functions
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| istyp | untyp | Typed at marker?
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| ishom | Homozygote?
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| alla | allb | First or second allele
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| commar | Maximum markers common with a relative
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| numtyp | anytyp | alltyp | number of genotypes
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| female | male | Indicate sex
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| isfou | isnon | Indicate if pedigree founder
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| num | nfound | family size/no. founders
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| famnum | index | Family or person index number
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| chosen | Used by the previous command
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| Macros
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| macro <nam> [<body>] | create or delete a macro
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| %<nam> | a macro variable
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| %% %0 %N %+N | macro function arguments
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| eval [<SEXPR>] | evaluate a Scheme expression
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| Command Iteration
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| <cmd> { <val1> [<val2> ...] } | Loop over set
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| Reading in Data
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| set datadirectory | Set data directory
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| set workdirectory | Set work directory
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| set impute on | off | Marker imputation
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| set errordrop on | off | remove nuclear family mendelian errors
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| set checking [sex] on | off | toggle error checking
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| set locus <nam> mar | xma | hap | qua | aff [<map_position> [<comments>]] | declare locus position,type
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| declare loci <num>(m | x | q | a) [<N>(m | x | q | a) ...] | batch declare loci (autoname)
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| set memory <num>(m | x | q | a) [<N>(m | x | q | a) ...] | preallocate memory for extra loci
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| rename <loc> [to] <new> | rename locus
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| read locus linkage <fil> | read Linkage locus file
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| read locus merlin <fil> | read Merlin locus file
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| read locus plink <fil> [not] | read PLINK .map file
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| read locus vcf <fil> [<start> [<end>]] | read VCF file locus information
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| read annotations <fil> [<var [><idx>]] | read VCF file INFO variable
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| read merlin <fil> | read Merlin pedigree file
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| read pedigree <fil> | read Sib-pair pedigree file
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| read linkage <fil> | read pre-Makeped pedigree file
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| read ppd <fil> | read post-Makeped pedigree file
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| read cases <fil> | read nonpedigree data file
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| read vcf <fil> [ped_id] | read VCF file IDs
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| read hapmap <fil> | read HapMap style genotypes file
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| read bin <fil> | read Sib-pair binary file
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| read plink <pre> | read PLINK .bed file
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| set sex marker <mar> | Sex informative marker
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| set twin <twin> [mer] | Zygosity or MZ twin indicator
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| set twin error <thr> <N> | MZ twin/duplicate test cutoffs
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| set liability <tra> <liab> <nlev> | declare liability classes for trait
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| set skiplines <slines> | Skip lines at head of pedigree file
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| order <loc1>.[to]..<locN> [$(m | x | h | q | a)[rm]] | reorder loci
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| set map <pos1>...<posN> | set marker map
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| set distances <dis12> <dis23>...<disN-1N> | set marker map
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| set chromosomes <chr1> [...<chrN>] | assign markers to chromosomes
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| read map <fil> | read map, guessing format
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| read chain <fil> | read UCSC chain filemap, and update map
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| read statistics [vcf] <fil> <var> | read in test statistics for loci
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| set frequencies <mar> [<frq1>...<frqN>] | set allele frequencies for a marker
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| set prevalence [<prev>|off] | fix population binary trait prevalence
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| run | process pedigree data
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| Subsetting Data
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| keep | drop <loc1>.[to]..<locN> [$m | x | h | q | a] | keep/drop useful/less loci
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| keep | drop where (mon|max|num|dis|r2|eve|pos|hwe|<str> | keep/drop useful/less loci
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| undrop <loc1>.[to]..<locN> [$m | x | h | q | a] | return loci to analysis
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| undrop where <str> | return loci to analysis
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| select [con | exa <npro> whe] <expr> | select pedigrees on criterion
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| select pedigree | id [not [in]] <ped1>...<pedN> | select on name
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| unselect [Nth] | return pedigrees to analysis (from Nth last selection)
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| pack [loc | ped] | delete dropped pedigrees and loci permanently
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| Transforming Data
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|---|
| edit <ped> <per> | all <loc> [to] <val1> [<val2>] | edit data
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| copy <ped1> <per1> <ped2> <per2> | copy individual data
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| merge <loc> [...<locN>] <fil> | merge data from phenotype file
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| merge genotypes <fil> | merge genotypes from file (one per line)
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| merge probabilities [<key>] <fil> | merge Beagle/Impute genotype probabilities
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| merge plink <pre> | merge data from PLINK genotype file
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| merge mac <fil> | merge data from MaCH dosage file
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| merge vcf <fil> [<buflen>] | merge data from VCF genotype file
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| merge fim <locfil> <genofil> | merge data from FImpute genotype file
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| update <loc> [...<locN>] <fil> | update data from phenotype file
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| delete <ped> <per> | all | set all data missing for person or
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| delete [<loc1>...<locN>] whe <expr> | set selected data missing
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| get <rel> <sum> <tra> [<new>] | get/save relatives trait value summary
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| recode [<mar> | $(m | x)] fre | recode alleles to 1..n by size/freq
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| recode [<mar> | $(m | x)] let | num | recode nt alleles to/from numbers
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| recode [<mar> | $(m | x)] ref [<tra>] | recode missing genotypes to reference homozygote
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| recode <loc> <val1>...<valN> to <new> | recode old values to new
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| combine <mar1>...<marN> [<thr>] | recode rare alleles
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| swap <mar> | swap SNP allele labels around
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| flip <mar> | recode SNP nucleotides to complementary strand
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| flip map <fil> | recode SNP nucleotides to match strand in reference VCF/GTF file.
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| flip fas <fil> | recode SNP annotation to match strand in reference FASTA file.
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| date (<yyyymmdd> jul) | (<num> greg) | julian date conversion
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| date [<tra>] [jul | greg | yea] | julian date conversion
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| standardize <loc> [fam] | standardize trait value
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| adjust | Note: superceded by residuals command. linear regress adjust
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| residuals <tra> on <loc1>...<locN> [com] | linear regress resid
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| predict <tra> on <loc1>...<locN> [com] | linear regress predicted
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| impute <tra> on <loc1>...<locN> [com] | linear regression imputation
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| impute <tra> | familial imputation (esp age)
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| kaplan-meier <tra> <cen> [res] | survivor function estimate
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| quantile_normalization <tra> ...<tra>] | perform quantile normalization
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| normality <tra> [...<tra>] | test normality of trait values
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| rank <tra> <rank> | rank of trait value
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| blom <tra> <blom_score> | inverse normal transform
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| simulate <mar> [<linked_to>] [<Nall> | <frq1>.<frqN>] | simulate a marker
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| simulate <tra> [<h2>] [<linked_to>] | simulate a trait
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| simulate qtl <tra> <mar> [<h2>] | simulate qtl genotypes
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| simulate pedigrees [<nped> [<ngen> [<min_kids> [<max_kids> ]]]] | simulate pedigrees
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| permute <tra> | permute trait values within pedigrees
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| Transforming Pedigrees
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|---|
| nuclear [<maxsibs>] [gra] | convert to (trimmed) nuclear families
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| subpedigrees | divide into subpedigrees (if compound)
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| join <ped1> [...<pedN>] | join up pedigrees by shared IDs
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| prune <tra> [c_op <thr>] | prune unaffecteds
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| cases <tra> | divide into unrelated cases
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| unique_id [seq] | generate numerical IDs
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| Outputting Data
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|---|
| hash <ID_file> | <ped> <per> | search for IDs
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| print ped <ped1>...<pedN> [id <id1>...<idN>] | print data
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| write [gas] [<fil>] | write Sib-pair pedigree file
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| head | tail [[<skip>] <nrec>] | print head or tail of pedigree file
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| more [<nrec>] | page through pedigree file
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| write bin <fil> [com] | write Sib-pair binary file
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| write pap | write to PAP
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| write var | write MENDEL var file
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| write locus pap | write PAP locus file
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| write arlequin [par | all] <fil> | write Arlequin data file
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| write asp | tcl [dum] <fil> | write Aspex pedigree file
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| write beagle <fil> [fou|tri] | write Beagle type data file
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| write crimap <fil> | write Cri-map pedigree file
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| write csv <fil> [<sep> [<mis>]] | write CSV type file
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| write dot [<tra> [<gen>]] <fil> | write Dot graph file drawing pedigree
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| write fisher <fil> | write FISHER pedigree file
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| write gda <fil> | write GDA pedigree file
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| write gh [dum] <fil> | write Genehunter pedigree file
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| write haploview [dum] <fil> | write Haploview pedigree file
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| write linkage | pre [dum] <fil> | write Linkage pre-Makeped pedigree file
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| write mendel <fil> [tra] | write MENDEL pedigree file
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| write merlin [dum] <fil> | write Merlin pedigree file
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| write mim <fil> | write MIM pedigree file
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| write morgan <fil> | write MORGAN pedigree file
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| write pap | write PAP trip.dat and phen.dat
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| write ped <fil> | write Sib-pair/GAS pedigree file
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| write phe <fil> | write FBAT/Sibs type phenotype file
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| write pli <pre> [<tra>] | write PLINK .bed .fam .bim files
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| write ppd [dum] <fil> | write Linkage post-Makeped pedigree file
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| write ram <tra> | write LDL_rams ped and dat files
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| write sage <fil> | write SAGE pedigree file
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| write sas <fil> [<sep> [<mis>]] | write SAS script with inline data
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| write sib-pair <fil> [merge] | write Sib-pair script with inline data
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| write solar <fil> [phe] [nop] | write Solar type pedigree file
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| write structure <fil> [fou] | write Structure type data file
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| write locus asp | tcl <fil> | write ASPEX locus file
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| write locus eclipse <fil> | write Eclipse data file
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| write locus fisher <fil> | write FISHER locus file
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| write locus gas <fil> | write GAS locus file
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| write locus loki <fil> [<pedfil>] | write Loki "prep" control file
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| write locus gh <fil> [dum] [xli] | write Genehunter locus file
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| write locus haploview <fil> | write Haploview info file
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| write locus linkage <fil> [dum] [xli] | write Linkage locus file
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| write locus mendel <fil> [tra] | write MENDEL locus file
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| write locus merlin <fil> | write Merlin locus file
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| write locus morgan <fil> | write MORGAN locus file
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| write locus pap | write PAP header.dat and popln.dat
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| write locus relpair <fil> | write RELPAIR locus file
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| write locus sage <fil> | write SAGE locus file
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| write locus sibpair <fil> [<pedfil>] | write Sib-pair script
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| write locus structure <pedfil> [<locfil>] | write Structure mainparam
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| write locus superlink <fil> [dum] [xli] | write Superlink locus file
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| write map mendel <fil> | write MENDEL map file
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| write map loki <fil> | write Loki parameter file
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| write map mendel <fil> | write MENDEL map file
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| write map merlin <fil> | write Merlin map file
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| write map solar <fil> | write Solar map file
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| write var <fil> | write MENDEL var file
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| Analysing pedigrees
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| generations [<qua_tra> [rev]] | summarize pedigree(s) and (save) generations
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| loops | show marital or inbreeding loops
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| relatives <ped> <id> | show immediate relatives of index
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| ancestors <tra> [c_op <thr>] | common ancestor of most probands
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| Checking data
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| test dob <tra> [greg] [<thr>] | Check consistency of DOBs
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| test age <tra> [<thr>] | Check consistency of ages
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| test sex | Check sex using markers
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| test haploid | Check Mendel errors
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| test locus <mar1> [...<marN>] | Check autosomal/X-linked Mendel errors
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| test map [(merge [<thresh>]) | <fil>] | Check map for duplicate positions
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| test vcf <fil> [ped_id] | Compare genotypes to VCF file
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| test fimpute <locfil> <genfil> [ped_id] | Compare genotypes to FImpute file
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| test flips map|fas <fil> | test strand flips versus reference.
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| test strand <mar1> [...<marN>] | test and repair strand problems
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| test duplicate [ids [merge]] [<indic>] | test for MZ twins or duplicates using markers
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| Analysing data
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| typed [<tra>] | Number genotyped stratified by a trait
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| frequencies | describe [snp | <loc1>..<locN>] | descriptive statistics
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| mcf <loc> | $m | MCEM allele frequencies
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| count [whe] <expr> | count where expression true
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| print [whe] <expr> | print data where expression true
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| plot <tr1> <tr2> | scatterplot
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| hist <tr1> [<nbins>] | histogram
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| mean | correlation [<loc1>..<locN>] | phenotypic means and correlations
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| pca [<loc1>..<locN>] | phenotypic principal components analysis
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| tab <tr1> [<tr2>...<trN>] | contingency table
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| tab ped <tra> | tabulation by pedigree and Tarone test
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| llm <tr1> ... [<tr1> * <tr2>...] [-1] | log-linear model of a contingency table
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| kruskal-wallis <qua tra> <loc> | Kruskall-Wallis test
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| regress <qua tra> on <loc1>.[to]..<locN> | linear regression
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| regress <bin tra> on <loc1>.[to]..<locN> [off <off>] [sim] | logistic regression
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| regress <tra> on <loc1>.[to]..<locN> [off <off>] poisson [sim] | poisson regression
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| regress <tra> ... [off <off>] [(exponential | weibull <cens>)] [shape <sha>] [sim] | survival regresssion
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| clreg <bin tra> on <loc1>.[to]..<locN> [ped|stratum <str>] | conditional logistic regression
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| mixture <qua tra> [[<num>] [nor | poo | exp | poi]] | test admixture
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| lifetable <sta> <end> <cen> [<wid1> [<wid2>]] [time] [cov <cov>] | life table
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| surv <onset> <cen> [<cov1> [...<cov2>]] | logrank test
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| Analysing genetic data
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|---|
| frequencies | describe [snp | <loc1>..<locN>] | descriptive statistics
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| mcf <loc> | $m | MCEM allele frequencies
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| blu <loc> [<tra> [<c_op> <thr>]] | BLUE allele frequencies
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| gpe <mar> [<dose>] | Estimate genotype probabilities or expected gene dose
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| segregation <mar> [unp] | Tabulate marker segregation
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| haplotypes <mar1> <mar2> <new>
[<thr>] | haplotypes for SNPs in complete LD
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| triads | show triad-phaseable haplotypes
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| mztwin [zyg <co> [<thr>]] [clean | delete] | MZ pair genotype discordance | drop one member
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| summary [<N_tests> | plot [<fil>]] | summarize last genetic test
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| Genetic equilibria
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|---|
| hwe [fou] [<mar1> ..[to].. <mar1>] [$(m | x)] | test HWE
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| homoz <tra> [<c_op> <thr>] | marker homozygosity
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| multihomoz <tra> [<c_op> <thr>] | multipoint homozygosity
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| fstats <tra> [fou] | Population genetic F-statistics
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| mds <ax1> [... <axN>] | Marker IBS multidimensional scaling
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| pca ibs <ax1> [... <axN>] | Marker IBS principal components analysis
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| dis [[<marker locus 1>] <marker locus 2>] | intragametic association
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| neff [[<map window>] <critical P>] | effective number (due LD) of marker tests
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| Kinship
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|---|
| kinship [pai | inb] [<tra> [c_op <thr>]] | kinship/inbreeding coefs
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| ibd <loc> [pai] | IBD matrix for marker
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| ibs <loc> [pai] | IBS matrix for marker
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| hbd <loc> [<coe>] | homozygosity-by-descent at marker
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| cksib | sib pair ibs sharing at multiple markers
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| share [pai] | rel pair ibs sharing at multiple markers
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| Twin analyses
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|---|
| mztwin [zyg <co> [<thr>]] [clean | delete] | MZ pair genotype discordance | drop one member
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| twin <tra>[<c_op> <thr>] | analyse twin correlations/concordances
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| kendalltau <age> <tra>[<c_op> <thr>] | analyse twin age at onset
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| Variance components and segregation analysis
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|---|
| davie <tra> <pro> | segregation ratios under ascertainment
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| varcomp <tra> [[a][c][d]e] [cov <var1>..+ <varN>] | Variance Components trait analysis
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| lrt | compare last 2 models fitted (mix/VC/GLM/GLMM)
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| blup <tra> <h2> | BLUP for AE variance components model
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| fpm <tra> [<c_op> <thr>] [nqtl <nqtl>] [p] [a] [d] [g] [c] [s] | MCMC mixed/SML/finite polygenic
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| fpm <tra> ... [(p | g | a | c | s)va | AA | AB | BB | mu | var <val>] | MCMC fpm start values
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| fpm <tra> ... [fixed p | a | c | d | e | g | m | mu | s | var | MCMC fpm fixed pars
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| fpm <tra> ... [lin logit | probit | ln | mft] [lik gau | bin | poi] [cov <var1> [+ <var2>...] | MCMC fpm
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| fpm <tra> ... [lik wei cen <tra>] | MCMC fpm survival analysis
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| Association
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|---|
| assoc <tra> [<c_op> <thr> | cat] [fou] [gen] | allelic/genotypic association with a trait
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| mito|yhap <tra> [<mar1> [..<marN>]] | Mitochondrial/Y-chromosome haplotype association with a trait
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| rare <tra>|<marker> | rare allele pooling and association
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| skat <tra> [mad|bet] | rare allele combined association
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| mgt <tra> [<marker>] | variance components allelic association
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| wqls <tra> | WQLS allelic association
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| mqls <tra> [<c_op> <thr>] [<prev>] | MQLS allelic association
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| tdt <tra> [<c_op> <thr>] [pat | mat] | several TDTs
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| hrr <tra> [<c_op> <thr>] | Haplotype Relative Risk
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| schaid <tra> <mar> [<all>] | Schaid & Sommer HWE test
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| sdt <tra>[str <str>] | sibship disequilibrium test
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| trend <tra> <mar> [perm] | Jonckheere-Terpstra trend test
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| Linkage
|
|---|
| asp <tra> [<c_op> <thr>] | affected sib-pair IBS and IBD linkage analysis
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| penrose <loc1> <loc2> | Penrose sib-pair linkage
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| apm <tra> [<c_op> <thr>] [ibd | ibs] | IBS or IBD NPL analysis
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| sibpair <tra> [<wei>] [sim] [cor <r> [mea <m>] [sd | var <v>]] | regression-based QTL linkage
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| twopair <tra> <loc1> <loc2> <theta> | two-point Haseman-Elston
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| qtlpair <tra> [full [cqe] [cov <var1>..+<varN>]] | sibs or pedigree VC linkage
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| varcomp <tra> [aqe <mar1>..+ <marN>] [cov <var1>..+<varN>] | Variance Components linkage analysis
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| linkage [<loc1> [<loc2>]] | intermarker sib pair linkage
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| lod <loc1> <loc2> [<theta>] | intermarker lod score linkage
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