Exons:
Relevant bits of information for using the MUSC Shared Resource,
 the BioMolecular Computing Resource (BCR).

Exon_63 QTDT- Quantitative TDT  programs at MUSC.

(c) 1998-2000 Goncalo Abecasis (goncalo@well.ox.ac.uk)

This program implements tests described by
Abecasis et al, Am J Hum Genet 66:279-292 (2000)
Allison, in Am J Hum Genet 60:676-690 (1997) [TDTQ5]
Fulker et al, in Am J Hum Genet 64:259-267 (1999)
Monks et al, ASHG meeting (1998)
Rabinowitz, in Hum Hered 47:342-350 (1997)


There are several programs :
 
qtdt- Quantitative TDT 2.1.11 
prelude- Preprocessor for external IBD sources
pedstats- Pedigree Statistics - 
finale- Postprocessor for external IBD sources

There is an on-line 
manual and documentation.
      
        

These are all programs with plain text 
user interfaces ( ie no fancy GUI).

The following parameters are in effect:
                QTDT Data File :        qtdt.dat (-dname)
            QTDT Pedigree File :        qtdt.ped (-pname)
          QTDT IBD Status File :        qtdt.ibd (-iname)
            Missing Value Code :         -99.999 (-xname)
                    Covariates :  USER SPECIFIED (-c{p|s|u|-})
             Association Model :      ORTHOGONAL (-a[a|f|m|o|p|r|t|w|-])
          Full Model Variances :    NOT MODELLED (-v{e|c|n|t|g|a|d|-})
          Null Model Variances :    NOT MODELLED (-w{e|c|n|t|g|a|d|-})
   Genetic Dominance Parameter :             OFF (-g[+|-])
      Parent of Origin Effects :            NONE (-o[f|t|m|p|-])
      Monte-Carlo Permutations :               0 (-m9999)
             Numeric Minimizer : NELDER AND MEAD (-n[n|p])
             First Allele Only :             OFF (-1[+|-])

NB: this program will not run on quark.musc.edu.
    It will run on erg2, janus and photon.

Users supply their own *.dat, *.ped and *.ibd files

Here are five example files

 sibs.dat
 sibs.ped
 sibs.ibd
 trios.dat
 trios.ped



In the following example, input files sibs.dat,sibs.ped and sibs.ibd
are indicated by preceding each name with a minus sign and a letter:

USAGE at the UNIX command line type: 

 qtdt -dsibs.dat -psibs.ped -isibs.ibd

note that the file named "sibs.dat" is preceded by  "-d"
in the command line eg "-dsibs.dat" and so forth.     
 

The BCR at the Medical University of South Carolina
URL: http://bcr.musc.edu/
Last modified: June 19, 2000- ESH

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