QTDT - Frequently Asked Questions

1. How do I reference QTDT?

To original reference for QTDT is Abecasis GR, Cardon LR, Cookson WO (2000) A General Test of Association for Quantitative Traits in Nuclear Families. Am J Hum Genet 66:279-292. Additional methods implemented in QTDT for the analysis of extended pedigrees and discrete traits are documented in Abecasis GR, Cookson WO and Cardon LR (2000) Pedigree tests of transmission disequilibrium. Eur J Hum Genet 8:545-551.

2. Why should I register my copy of QTDT?

Well, all software programs are buggy... and QTDT is probably no exception. If we find something wrong, we need your e-mail address to let you know. This information is also used to gauge the level of interest in the project and helps decide whether to invest time making QTDT even better or, perhaps, go back to the lab and do some real work.

3. Do I need a license to use QTDT?

QTDT is available free for both commercial and non-commercial use, no license is required. However, note that redistribution of the QTDT source code or binaries is not allowed. If you do use QTDT, please register.

4. Why are some alleles not tested?

The standard version of QTDT only attempts to estimate allele effects when at least 30 informative individuals are available. For most tests, informative individuals are phenotyped offspring with at least one heterozygous parent. Maximum likelihood tests can be unreliable on smaller datasets, but it is possible to analyse smaller datasets by changing value of the QtdtOptions::minProbands parameter in the QtdtOptions.cpp file and recompiling QTDT. If you do decide to do this, you should calculate empirical significance levels when evaluating evidence for association at rare alleles.

5. Can I send QTDT output to a file?

To send QTDT output to a file, you can either redirect output to a file, with the ">" redirect operator, e.g.:

  prompt> qtdt -d datfile -p pedfile > outfile

Or, in standard Unix systems, you can get output both to the screen and a file by piping QTDT output through the tee utility:

  prompt> merlin -d datfile -p pedfile -m mapfile | tee outfile

6. Can I disable testing of some markers, phenotypes or covariates without generating a new pedigree file?

Yes! The simplest way to skip over a trait, covariate or marker during analyses is to make a small edit to the data file, as follows: if you want to disable a particular covariate or trait, replace the the "C covariate_name or "T trait_name" row in the data file with "S covariate_name" or "S trait_name". The "S" label stands for SKIP COLUMN and the covariate or trait will be ignored. If you want to disable a particular marker, replace the "M marker_name" in the data file with "S2 marker_name". The "S2" label stands for "SKIP TWO COLUMNS".