All the Sib-pair Commands

Global Commands Reading in Data
Utilities Subsetting Data
Basic Language Objects Transforming Data
Operators Transforming Pedigrees
Mathematical Functions Outputting Data
Data Functions Analysing pedigrees
Macros Checking data
Command Iteration Analysing data
Analysing genetic data
Genetic equilibria
Twin analyses
Variance components and
segregation analysis

Global Commands
echoprint 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
infoprogram 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 locilocus information
show spectraTabulate loci by allelic spectrum
show pedigreestabulate pedigrees
show idstabulate IDs
show chromosomecurrent chromosomes
show mapshow linkage map
show macroslist macros
show missingcount missing data for each locus
timetotal elapsed time
set timertime procedures
include [<fil>] read commands from file
output [<fil>] divert text output to a file
last [<num>] command history
quitexit program
set promptdisplay prompt
set gui on | offactivate GUI
set ndecimal_widthoutput 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
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
Alleles are 1..999, A-Z, a-z
( ) ; : Grouping and precedence
:Separate sequence of expressions
* | / | + | - | ^Arithmetic
< | > | =< | => | ge | le | eq | == | ne | ^= | and | orComparison
if | thenConditional statement execution
Mathematical Functions
log | sqrt | exp | sin | cos | tan | asin | acos | atan | absMaths functions
pnorm | qnormStatistical functions
int | round Truncating functions
rand | rnormUniform or Gaussian random numbers
greg | julian Date functions
Data Functions
istyp | untypTyped at marker?
alla | allbFirst or second allele
commarMaximum 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 | indexFamily or person index number
chosenUsed by the previous command
macro <nam> [<body>] create or delete a macro
%<nam> a macro variable
%% %0 %N %+Nmacro 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
adjustNote: 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> | $mMCEM 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> | $mMCEM allele frequencies
blu <loc> [<tra> [<c_op> <thr>]] BLUE allele frequencies
gpe <mar> [<dose>]Estimate genotype probabilities or expected gene dose
segregation <mar> [unp]Tabulate marker segregation
haplotypes <mar1> <mar2> <new> [<thr>] haplotypes for SNPs in complete LD
triads show triad-phaseable haplotypes
mztwin [zyg <co> [<thr>]] [clean | delete] MZ pair genotype discordance | drop one member
summary [<N_tests> | plot [<fil>]] summarize last genetic test
Genetic equilibria
hwe [fou] [<mar1> ..[to].. <mar1>] [$(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 [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
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
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