To further assist you:
In order to create your own GCmodel file, you need three things:
- cal_gc_snp.pl script from GitHub
- GC content information for ovine (Ovis aries)
- SNP marker information
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cal_gc_snp.pl can be downloaded from PennCNV's GitHub page: https://github.com/WGLab/PennCNV/blob/master/cal_gc_snp.pl
GC content information for ovine is available from UCSC for build1 and build3 of the sheep genome:
- http://hgdownload.cse.ucsc.edu/goldenPath/oviAri1/database/gc5Base.txt.gz (buiid 1)
- http://hgdownload.cse.ucsc.edu/goldenPath/oviAri3/database/gc5BaseBw.txt.gz (build 3)
Once you download these, unzip, and then sort (and save a new copy) using: sort -k 2,2 -k 3,3n <input > output
The SNP file you should already have for your microarray version. It needs to be of the form:
Name Chr Position
rs1000113 5 150220269
rs1000115 9 112834321
rs10001190 4 6335534
rs10002186 4 38517993
rs10002743 4 6327482
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You then generate the GCmodel file with:
perl cal_gc_snp.pl gc5BaseBw.sorted.txt SNPfile.txt -output ovine.gcmodel
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Kevin Blighe
Hi I need to a GC model file for adjust Genomic wave in result of penncnv software.my data is about ovine high- density 600k chip, so it doesnt worked with GCmodel in software package because it is for human data.
Did you just create an extra account?
This script, part of PennCNV, can apparently generate a GCmodel file for you: https://github.com/WGLab/PennCNV/blob/master/cal_gc_snp.pl
Please take a look.
Edit: I also recommend that you contact the PennCNV developers and / or Affymetrix, as they may be able to quickly supply this file to you
I have added to my answer (below), effectively showing you exactly what you need to do