QTDT - IBD File

QTDT includes a very simple IBD engine that can calculate calculate single point IBD estimates only when both parents have been genotyped. This is often inappropriate. The ibd input file allows QTDT to interface with more sophisticated IBD estimators.

The format for this file is:

  <family> <person1> <person2> <marker> <z0> <z1> <z2>

Where <z0>, <z1> and <z2> denote the probability that <person1> and <person2> in <family> share 0, 1 or 2 alleles IBD at the marker locus <marker>.

For convenience two additional utilities are included for interfacing with Simwalk2 (version 2.60), a program that uses multipoint information to estimate IBD in most types of families. These utilities can also be used to interface with genehunter2 in data sets consisting of smaller families.

Prelude prepares data and pedigree files in QTDT format to be analysed by SimWalk2 or Genehunter. Finale collects the results of this Simwalk2 analysis into a single IBD file that is ready for input into the QTDT program.

Prelude takes the following parameters:

• The names of compatible pedigree (-p) and data (-d) files;
• The recombination fraction between markers (-t) or a map file(-m) in MERLIN format. Map positions are assumed to be in Haldane centiMorgans.;
• The method for estimating allele frequencies (-a[a|e|f], where -aa denotes the overall allele frequency in the pedigree, -ae denotes the assumption that all alleles have equal frequency and -af denotes that only founder alleles should be used to estimate allele frequencies.)

If your markers are not equally spaced, an alternative to supplying a MERLIN format map file is to edit section 000015 of BATCH2.DAT file (which includes the Simwalk2 parameter specifications). See the Simwalk2 documentation for help on this.

For example if your pedigree and data files were called mydata.ped and mydata.dat, you might run the following sequence of commands:

   prompt> prelude -d mydata.dat -p mydata.ped -t 0.001 
   prompt> simwalk2
   prompt> finale IBD-01.*
   

Genehunter (v2) support.

Prelude creates a genehunter compatible linkage format pedigree (linkage.ped) and data (linkage.dat) files. These files include an unlinked, uninformative marker -- named "undrop" (sic) -- to stop genehunter from excluding family members from analysis.

An additional file (genehunter.in) includes a series of commands instructing genehunter to carry out IBD estimation. If your markers are not equally spaced, you should either supply a MERLIN format map file to prelude or edit the USE command in this file.

For example if your pedigree and data files were called mydata.ped and mydata.dat, you might run the following sequence of commands:

   prompt> prelude -d mydata.dat -p mydata.ped -t 0.001 
   prompt> gh2 < genehunter.in
   prompt> finale genehunter.in