Sib-pair Command: write locus

Class	Analysis and data manipulation command
Name	write locus
Arguments	<type>	<file>	[<arg>]
	aspex|tcl	<locus file name>
	beagle
	fimpute		[chip< chip>]
	fisher
	gas
	haploview
	linkage|gh		[dummy] [xlinked]
	loki		[<pedigree file name>]
	mendel		[trait]
	merlin
	relpair
	sage		[par]
	sib-pair		[<pedigree file name>]
	structure		[<pedigree file name>]
	superlink		[dummy] [xlinked]

Use of the keyword gas writes a GAS type locus file from the current dataset;

beagle writes a Beagle marker file: each record is the marker name, position (bp), allele names.

fimpute writes a FImpute locus file. The chip keyword preceded the trait indicating the SNP array or genotyping method for each marker.

fisher writes a locus file from the current dataset suitable for use by the program FISHER;

haploview writes an "info" file, giving the marker position as the first word of the annotation if it is numerical, or the map position multiplied by 10⁶;

linkage writes a locus file from the current dataset suitable for use by the LINKAGE (and FASTLINK) programs; gh writes the same as linkage save that map distances are in cM. The dummy option is used when the first trait is a dummy trait generated by

write linkage <file> dummy

The keyword loki writes a control file for LOKI's prep program;

mendel writes a locus file from the current dataset suitable for use by the programs MENDEL or SIMWALK (with binary traits defaulting to a factor, but given as a diallelic locus if the trait modifier is present);

merlin for MERLIN;

relpair writes the RELPAIR format (modified from that for MENDEL): it infers chromosome number from the map position (as multiples of 1000) or from the locus name (if it takes the form of "DxSxxx").

sage writes a locus file from the current dataset suitable for use by the SAGE package, or a parameter file (if the par modifier is present) as used by the more recent SAGE programs;

sib-pair writes a Sib-pair style script;

superlink writes a LINKAGE style locus file modified for the SUPERGH option of SUPERLINK;

structure writes the mainparams file required by the STRUCTURE program.

tcl or aspex writes the tcl command file required by ASPEX programs such as SIB_PHASE;

Example:

write locus merlin merlin.dat

See also:

set liability	Declare a quantitative trait to be a liability class indicator
write	Write a pedigree file