GWAS - CEL to call

source: penncnv wget http://www.openbioinformatics.org/penncnv/download/penncnv.latest.tar.gz wget http://www.openbioinformatics.org/penncnv/download/gw6.tar.gz from http://www.affymetrix.com/support/developer/powertools/index.affx wget http://www.affymetrix.com/Auth/support/downloads/library_files/genomewidesnp6_libraryfile.zip
 * 1) Download the Affymetrix Power Tools (APT) software package
 * 1) decompressed files to the lib/ directory

/sdc/analysis/apt-1.14.4.1-amd64-pc-linux/bin/apt-probeset-genotype \ -c /sdc/analysis/penncnv/lib/GenomeWideSNP_6.cdf \ -a birdseed \ --read-models-birdseed /sdc/analysis/penncnv/lib/GenomeWideSNP_6.birdseed.models \ --special-snps /sdc/analysis/penncnv/lib/GenomeWideSNP_6.specialSNPs \ --out-dir out \ --chrX-probes /sdc/analysis/penncnv/lib/GenomeWideSNP_6.chrXprobes \ --chrY-probes /sdc/analysis/penncnv/lib/GenomeWideSNP_6.chrYprobes \ --cel-files out/listfile.test.txt

Example quick plot: Scatter Plot < Main Page