Appendix 1

SOLAR Command Descriptions

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

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
evdinev	I/O for EVD data
evdinx	I/O for EVD data
evdiny	I/O for EVD data
evdinz	I/O for EVD data
evdmat	I/O for EVD data
evdout	I/O for EVD data
example	Copy the SOLAR example to the current working directory
exclude	Excude phenotypes from use as covariates by automodel
factorial	Compute factorial
fakedata	Generate fake pedigree/phenotypes file for testing memory required
faketraits	Generate fake pedigree/phenotypes file for testing memory required
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-matrix	Describe csv matrix file format 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
fphi	Fast test and heritability approximation (Experimental)
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
intraitclass	Set up polygenic model with class specific parameterization
invert	transpose on MathMatrix or 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
mask	To read image mask file and set current voxel
matcrc	Prepend pedindex checksum (CRC) to the beginning of a matrix file
mathmatrix	Create and use matrix objects in algebraic computations
matrix	Set up sample matrix (phi2 etc.) or math matrix
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
polyvoxel	polygenic analysis of image data
power	Perform power calculations (or MathMatrix power operation)
putsa	Write to file and/or terminal without having to open and close
putsat	Write to file and/or terminal without having to open and close
putsnew	Write to file and/or terminal without having to open and close
putsout	Write message to terminal and/or file [obsolescent]
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
retext	Translate files with Old Mac line terminators to unix terminators
retextpc	Translate files with Old Mac line terminators to unix terminators
save	save
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)
transpose	transpose on MathMatrix or comma delimited file
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
vcfinfo	extract per-genotype meta information from vcf file
vcfselect	extract genotype data from vcf file (HIGHLY EXPERIMENTAL!)
verbosity	Set the output verbosity.
voxel	To set and save current voxel position
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)