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