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

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• motivation

  LCP (linkage control program) is an auxiliary program for LINKAGE . On a MS-WINDOW system, LCP generates a "batch file", and on a UNIX system, it generates a "shell script". A user of the LINKAGE program is always instructed to run LCP first. Then the user should run the "batch file" or "shell script" to proceed the analysis.

  The most frequently chosen mode in LCP is to set up two-point analyses for each of the markers on a chromosome. This mode can be easily emulated by a Perl script, making LCP unnecessary.

• set up

  Another LINKAGE auxiliary program LSP (linkage setup program) is required. Unlike LCP, LSP does not require a graphic interface.

  The UNKNOWN program from LINKAGE/FASTLINK is also required.

  Of course, to run LINKAGE program, you need a LINKAGE parameter file and a LINKAGE pedigree file ( post-MAKEPED)

  If the chromosome number is (e.g.) 17, the name of the LINKAGE parameter file is chr17.dat, and that of the LINKAGE pedigree file is chr17.ped.

• the Perl script (no_lcp.pl)

• notes on the script

  The crucial part of the script is to feed a few lines of input to the LSP program. And it is done by the "open(README | $lsp )" and "print README $arg".

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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)

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