Appendix 1

SOLAR Command Descriptions

about	empp	if_global_exists	mibddir	putsout	sporadic
allcovar	epistasis	if_parameter_exists	miniplot	qtld	sporclass
allsnp	example	inormal	model	qtnm	spormod
alnorm	exclude	interval	mu	quadratic	startclock
ascertainment	factorial	invert	multipoint	read_arglist	stats
automodel	fformat	is_nan	needk2	read_model	stats_get
bayesavg	field	joinfiles	newmod	read_output	stepfor
benice	file-freq	key	newtcl	register	stepup
blank	file-map	linkgsd	normal	relatives	stopclock
boundary	file-marker	linkmod	null	relpairs	string_imatch
boundary-notes	file-pedigree	linkqsd	nulln	remlist	stringplot
catenate	file-phenotypes	linkqsd0	old_zscore	remove_global	stringsub
change-notes	finemap	load	omega	residual	tablefile
chi	fix	loadkin	option	save	tclgr
chinc	freq	lod	outdir	scale	tdist
chromosome	full_filename	lodadj	parameter	screencov	timediff
clod	grid	lodn	ped2csv	selectfields	toscript
combinations	gridh2r	lodp	pedigree	selectrecords	trait
constraint	gsd2h2q	loglike	pedlike	setappend	twopoint
copybin	gsd2h2r	madj	pedlod	setxor	upgrade
countfields	gsd2sd	map	perdelta	shortcut	usage
covariate	h2power	marker	perturb	showproc	usort
d2e	help	markertest	phenotypes	siminf	verbosity
d2e2	helpadd	matcrc	plot	simqtl	whoranch
define	hlod	matrix	plotqtld	slod	zs
deputy	house	maximize	plotqtn	snp	zscore
discrete-notes	howmanyranch	memory	polyclass	snphap
doc	ibd	mg_topedsys	polygenic	solarfile
dominance-notes	ibddir	mga	polygsd	solarmodel
doranch	ibdoption	mgassoc	polymod	solartcl
drand	ibs	mibd	power	solarversion

about	Copyright, authors, and disclaimers
allcovar	Set up all non-trait variables as covariates
allsnp	Include all snps as covariates in current model
alnorm	Evaluates the tail of normal curve
ascertainment	Describe ascertainment correction using proband(s)
automodel	Default model setup
bayesavg	Perform bayesian oligogenic model averaging
benice	Lower priority of SOLAR to allow more CPU for other jobs
blank	Blank individuals according to variable data conditions
boundary	Change artificial boundary heuristics
boundary-notes	Discuss boundary error resolution strategies
catenate	Concatenate strings
change-notes	Display recent changes
chi	Compute probability for a chi-square value
chinc	Compute probability for a noncentral chi-square value
chromosome	Select chromosome(s) for multipoint scan
clod	Calculate LOD score
combinations	Make a list or count combinations of integers 1..N of size K
constraint	Create, list, or delete constraints
copybin	Install new executable file without disturbing current users
countfields	determine consistency of number of columns in a comma delimited file
covariate	Set up covariates (independent variables).
d2e	convert Fortran D style exponents to E form
d2e2	convert Fortran D style exponents to E form
define	Define an expression to be used in place of a trait or covariate
deputy	Make limited user key (for deputy registrars)
discrete-notes	Describe support for discrete traits
doc	Find the SOLAR documentation
dominance-notes	Find dominance documentation
doranch	execute a script on every ranch machine (usually for /tmp cleanup)
drand	Return a random floating-point number between 0 and 1
empp	Calculate an empirical p-value from lodadj results
epistasis	Use command: multipoint -epistasis
example	Copy the SOLAR example to the current working directory
exclude	Excude phenotypes from use as covariates by automodel
factorial	Compute factorial
fformat	Replace Tcl format with fixed width fields for numbers
field	Allow non-standard user data field names
file-freq	Describe frequency data file requirements
file-map	Describe map data file requirements
file-marker	Describe marker data file requirements
file-pedigree	Describe pedigree data file requirements
file-phenotypes	Describe phenotypes data file requirements
finemap	Set fine mapping threshold for multipoint
fix	Constrain a parameter to its current value
freq	Process the allele frequency data.
full_filename	Prepend the maximization output directory name to filename(s)
grid	Find the highest likelihood in the vicinity of marker(s)
gridh2r	Find the highest likelihood in the vicinity of marker(s)
gsd2h2q	Convert esd,gsd,[qsd1] parameters to standard parameters
gsd2h2r	Convert esd,gsd,[qsd1] parameters to standard parameters
gsd2sd	Convert esd,gsd,[qsd1] parameters to standard parameters
h2power	Perform heritability power calculations
help	Display instructional messages
helpadd	Explain how to add more help messages to SOLAR
hlod	Heterogeneity test for linkage
house	Enable analysis of household effects
howmanyranch	Show how many ranch machines a user is using
ibd	Compute marker-specific IBDs.
ibddir	Set directory in which IBD matrix files are stored
ibdoption	Set or display IBD processing options.
ibs	Compute marker-specific IBS matrices.
if_global_exists	Check if a Tcl global variable exists
if_parameter_exists	Check if a parameter exists without creating it
inormal	Save inverse normal transformation to a file (see also define)
interval	Set cM interval and range for multipoint scanning each chromosome
invert	Row and column inversion on comma delimited file
is_nan	Check if value is NaN (Not a Number)
joinfiles	Join files horizontally based on ID's
key	Make user key
linkgsd	Set up linkage model with esd, gsd, qsd parameters (EXPERIMENTAL)
linkmod	Set up parameters and constraints for multipoint linkage model
linkqsd	Set up linkage model with esd, gsd, qsd parameters (EXPERIMENTAL)
linkqsd0	Set up linkage model with esd, gsd, qsd parameters (EXPERIMENTAL)
load	Load a user data file (pedigree, phenotype, marker, etc.)
loadkin	Load a matrix named phi2.gz containing phi2 and delta7
lod	Calculate LOD score
lodadj	Use or calculate an empirical LOD adjustment
lodn	Calculate LOD score for current model relative to nullX
lodp	Change LOD preferences (such as conversion to 1df)
loglike	Get the log likelihood of the current model
madj	Apply current lodadj to a previous multipoint run
map	Process the map data.
marker	Process the marker genotype data.
markertest	Test markerfile for discrepancies; list blankable ID's
matcrc	Prepend pedindex checksum (CRC) to the beginning of a matrix file
matrix	Set up matrix variables (e.g. ibd, mibd, kinship)
maximize	Find the maximum loglikelihood of a model by adjusting
memory	Show total memory used by this SOLAR process
mg_topedsys	Convert comma delimited mga.out to pedsys format
mga	Run Measured Genotype (MG) association analysis for every SNP
mgassoc	Run Measured Genotype (MG) association analysis for every SNP
mibd	Compute multipoint IBDs.
mibddir	Set directory in which MIBD matrix files are stored
miniplot	Arrange miniature plots on a single page
model	Describe, save, or load a model
mu	Set or Display the Mu equation (trait value estimator)
multipoint	Perform a multipoint analysis.
needk2	Keep K2 (phi2) terms from MIBD matrices
newmod	Start a new model
newtcl	Recognize new or changed Tcl procedures in Tcl scripts
normal	Normal distribution functions
null	Return an optimized parameter from null.mod
nulln	Return an optimized parameter from nullX.mod
old_zscore	The old zscore command to zscore current trait
omega	Sets the Omega (Covariance) equation directly
option	Set or read the value of model-specific options.
outdir	Set maximization output directory (overriding default)
parameter	Create, modify, or list parameter(s)
ped2csv	Convert Pedsys format file to comma delimited format
pedigree	Process the pedigree data.
pedlike	Calculate pedigree-specific loglikelihoods
pedlod	Calculate pedigree-specific LOD scores
perdelta	Set delta used by perturb
perturb	Perturb starting values for E2, H2r, and H2q's at bounds
phenotypes	Load the phenotypes file or display its variables
plot	Plot multipoint LOD scores, empirical LOD adjustments, or power
plotqtld	Plot qtld (qtld.out)
plotqtn	Plot qtn marginal tests (qtnm.out)
polyclass	Set up polygenic model with class specific parameterization
polygenic	Perform polygenic, sporadic, and/or household analysis
polygsd	Set up polygenic model esd and gsd parameters (EXPERIMENTAL)
polymod	Set up polygenic model with the standard parameters
power	Perform power calculations
putsout	Write message to terminal and/or file
qtld	Association analysis for snps
qtnm	Marginal tests for bayesavg -qtn
quadratic	Get the most recent quadratic form after a maximization
read_arglist	Read hyphenated optional arguments and argument-value pairs
read_model	Read a parameter value or likelihood from any saved model
read_output	Read variable statistics from maximization output file
register	Create registration key file
relatives	Show relationships of relative pairs included in analysis
relpairs	Show relationships of relative pairs included in analysis
remlist	Remove element from list by name
remove_global	Remove a global variable (so it no longer exists)
residual	Compute residuals for a maximized model and phenotypes file
save	Save data for future use
scale	scale a covariate variable, or disable default scaling
screencov	Perform polygenic analysis with covariate screening
selectfields	Select fields (columns) from data file(s) and copy to a new file
selectrecords	Select records from a file and copy them to a new file
setappend	Append only new elements to a list (keeping it like a set)
setxor	Perform exclusive-or (xor) on two sets (Tcl lists)
shortcut	Show command shortcuts legal in scripts
showproc	Show SOLAR procedure or write to a file
siminf	Simulate a fully-informative marker and compute its IBDs
simqtl	Simulate a QTL and (optionally) a linked marker
slod	Calculate slod (score-based LOD equivalent) on current model
snp	Process SNP data.
snphap	Compute SNP haplotypes and haplotype frequencies.
solarfile	Read data file applying "field" name mapping
solarmodel	Check SOLAR version compatibility of model
solartcl	Check SOLAR version compatibility of tcl file
solarversion	Display the SOLAR program version
sporadic	Perform polygenic, sporadic, and/or household analysis
sporclass	Set up polygenic model with class specific parameterization
spormod	Set up a sporadic model with the standard parameters
startclock	simple local timer (elapsed time)
stats	Get and/or show statistics for any variable in a file
stats_get	Retrieve statistics from list returned by stats
stepfor	Foward stepwise covariate screening
stepup	Covariate screening by Step Up algorithm, useful for QTN analysis
stopclock	simple local timer (elapsed time)
string_imatch	Case insensitive string match testing
stringplot	String plot of entire genome scan
stringsub	Simple verbatim string substitution (not regsub)
tablefile	Read data file in comma delimited or PEDSYS format
tclgr	Create xmgr session with pipe connection to SOLAR
tdist	Set up t option for robust estimation of mean and variance
timediff	Calculate seconds between two system time strings
toscript	Write previous commands to a script
trait	Select the trait (dependent variable)
twopoint	Perform "Twopoint" analysis on directory of ibd files
upgrade	Upgrade model files and scripts
usage	Print short "usage" message about a command
usort	Define unix sort program name
verbosity	Set the output verbosity.
whoranch	Show how many ranch machines each ranch user is using
zs	The old zscore command to zscore current trait
zscore	Zscore current trait(s) or covariate(s)