Perl as a Tool for Linkage Analysis

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
October 1999, San Francisco, CA
ABSTRACT

General information about running a Perl script on your computer

Example 1: Genome-wide linkage analysis

Example 2: Assigning liability class in LINKAGE

Example 3: Ranking individual family LOD scores

Example 4: Setting up two-point analysis in LINKAGE without using LCP

Example 5: Converting LINKAGE pedigree file to CRIMAP format

Example 6: A series of single-marker association studies using FASTEH+ (added on Nov 27, 2001)

If you are interested in a collaboration ...

There is a variety of tasks in daily linkage analysis of complex diseases. Most of Perl scripts listed here are illustrative or specific to our need. If you are interested in having a Perl script for your own task, such as automate all or a particular step in your linkage analysis, and need help from us, send an email to:

perl@linkage.rockefeller.edu .

For our service, we request a co-authorship if you are working for a non-profit organization such as a university or a hospital, and a fee if you are working for a biotech company.
We have noticed two other posters at the Annual Meeting of American Society of Human Genetics 1999 that address the similar issues.

One is: Mukhopadhyay, Almasy, Schroeder, Mulvihill, Weeks, "MEGA2: a data-handling program for fascilitating genetic linkage and association analyses" (poster # 2474). To quote from the abstract: "Not only must the data be converted to the proper format, but also the loci must be reordered into their proper order. To address this problem, we created MEGA2". Perl is perfect for this task! Their web site at Univ Pittburg is: http://watson.hgen.pitt.edu/ (the MEGA2 is not up yet - if you want a beta test version of the program, email to Dan Weeks at dweeks@watson.hgen.pitt.edu).

Another is: Hiekkalinna, Peltonen, "New program: AUTOSCAN 1.0 automated use of linkage analysis programs", (poster # 1416). To quote from them: "The use of linkage analysis programs consists of multiple file handling processes and production of input files specific for various statistical programs. This basically trivial process is time consuming and error prone since it repeats basic steps multiple times. Our aim was to develop a helper program to automate the tedious process of the creation of input files from genotype data of genome-wide scans, which would allow efficient analyses of several different phenotypic traits". To continue, they said: "In practice, this program enables the analyses of a whole genome-wide scan for all chromosomes in a single run". This is very similar to our example 1! Their web site at UCLA is: http://www.genetics.ucla.edu/software/autoscan/ .

More examples from other groups

Re-numbering individuals
Stefan Gaget, Institut de Biologie de Lille, France.
(added on Nov 16, 1999)

Removing untyped individuals
Stefan Gaget, Institut de Biologie de Lille, France.
(added on Nov 16, 1999)

Streamline ANALYZE runs
Juleen Cavanaugh, The Canberra Hospital, Australia.
(added on Jan 12, 2000)

This page is developed by Wentian Li and Fatemeh G Haghighi. Last update on January 12, 2000.