---

Example 1 - Genome-wide linkage analysis:

---

• motivation

  When markers on all 22 autosomal chromosomes are typed, one needs to run a linkage program (such as LINKAGE and GENEHUNTER) on each chromosome. Doing it manually is tedious! However, this repetition can be easily handled by Perl.

• set up

  You need to have a linkage program installed on your computer (LINKAGE/FASTLINK or GENEHUNTER)

  You have a pre-MAKEPED LINKAGE pedigree file (which contains pedigree as well as marker information) and a LINKAGE parameter file (which contains marker ordering, disease model, etc) for each chromosome.

  The name of the pedigree file for chromosome 1 is chr1.ped, that for the parameter file is chr1.dat; similar for other chromosomes.

  The names of subdirectories for all 22 chromosomes are simply 1, 2, ...

• a simple Perl script (genomewide_gh.pl) that runs GENEHUNTER for each chromosome

• notes on the script

  The "use Shell" line is to use a Perl module so that UNIX utility commands can be invoked within the script as if they were Perl subroutines: for example, "pwd()". If you are on Microsoft Window or MacOS, you may need an alternative way to do this.

---

This is a companion page for W Li, F Haghighi, "Perl as a tool for linkage analysis", American Journal of Human Genetics, supplement to vol 65, page A260 (1999) (poster number 1452 at the Annual Meeting of American Society of Human Genetics 1999, San Francisco, CA)

---