|Class||Analysis and data manipulation command|
|aspex|tcl||<locus file name>|
|loki||[<pedigree file name>]|
|sib-pair||[<pedigree file name>]|
|structure||[<pedigree file name>]|
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> dummywhile the xlinked option declares the markers to be all X-linked.
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;
write locus merlin merlin.dat
|set liability||Declare a quantitative trait to be a liability class indicator|
|write||Write a pedigree file|
|<< (write pap)||Up to index||>> (write locus pap)|