removing untyped individuals

Removing untyped individuals in pedigree files

Author(s)

Stefan Gaget of Institute of Biologie of Lille, France (email: gaget@mail-good.pasteur-lille.fr )
motivation

Some untyped individuals listed in the LINKAGE pedigree file may not be necessary for anything. It might be a good idea just to remove them from the file. (Other untyped individuals may be useful for supporting the pedigree structure, for example, the founders.)

set up

You need a LINKAGE pedigree file which may look like this:


....
3       1       0       0       1       2044     0  0    0  0
3       2       0       0       2       2045     0  0    0  0
3       3       1       2       1       2046     9 11   11 11
3       4       1       2       1       2047    11 13   11 11
3       5       1       2       2       2048    11 13   11 11
3       6       1       2       1       2049     0  0    0  0
....

the Perl script (removeind.pl)

output

The output is the new LINKAGE pedigree file with the untyped individual removed:


....
3       1       0       0       1       2044     0  0    0  0
3       2       0       0       2       2045     0  0    0  0
3       3       1       2       1       2046     9 11   11 11
3       4       1       2       1       2047    11 13   11 11
3       5       1       2       2       2048    11 13   11 11
....

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)