|
Download linkdatagen.pl
Download linkdatagen documentation
Download Affymetrix annotation files
(required by linkdatagen).
Download Affymetrix abridged annotation files
These files contain the SNPs ordered by chromosome and position. For each SNP both the Affymetrix SNPname and the rs name are given as well as both genetic and physical map positions.
Last Updated 5th of August, 2008
Linkdatagen.pl is a PERL script that generates LINKAGE style files for both
ALLEGRO
and MERLIN
using as input the genotyping calls generated by BRLMM, Affymetrix annotation files,
and a pedigree file. One of the assets of linkdatagen.pl is that it will allow the generation
of LINKAGE files without having to use the Affymetrix GCOS software.
Linkdatagen.pl allows the selection of one SNP per bin, where the user stipulates a
bin size that defines the bins across the genome. The SNP can be either randomly
chosen or be the SNP with the highest heterozygosity according to the HAPMAP
CEU (Caucasian data set). The latter in some sense gives the most informative dataset.
The generation of files with just subsets of markers is useful for linkage analysis using
the Lander-Green algortithm which assumes linkage equilibrium, an assumption that is
violated for groups of markers in all high density SNP chips.
The choice of binsize 0.5 yields ~6000 SNP markers and is thus roughly equivalent in
density to the Illumina linkage mapping panel. This binsize represents a safe choice of
marker number. Since the markers are chosen without paying any attention to HAPMAP
blocks there may still be the occasional false positive linkage peak due to linkage disequilibrium (LD). It is thus useful to also run the data with several random selections of markers. True linkage signals should persist; false linkage signals due to LD should not be consistent across marker sets. Alternatively examining the genetic map in the region of linkage will show how close the chosen markers are. In general false linkage peaks generated by LD will be much narrower than those expected for a true linkage peak.
The user can also elect to use all markers by specifying the binsize as 0.
To change the genetic model for ALLEGRO the user will have to scroll down to the
output subroutines and change the lines marked # CHANGED BY USER AS NECESSARY to reflect the appropriate parametric linkage model that they need. For MERLIN that param.tbl file would need to be changed, as this is the file that specifies the genetic model.
Linkdatagen.pl can handle 50K Xba, 50K Hind, 250K Sty, 250K Nsp, 5.0 (not tested yet) and 6.0 Affymetrix chip data.
Update 13/5/2008
Linkdatagen.pl can now handle all Affy chips and also produce PREST and MORGAN input files.
This distribution now includes all the Affy annotation files (not quite the latest one from the Affymetrix website, but ones that work).
Annotation files should all be put together in a directory specified for linkdatagen.pl by the command –annot_dir.
Email bug reports & questions to Melanie Bahlo (bahlo@wehi.edu.au).
If you use this program please acknowledge by referencing the website.
|
