A bioinformatic filter for improved base-call accuracy and polymorphism detection using the Affymetrix GeneChip® whole-genome resequencing platform

Pandya, Gagan A.; Holmes, Michael H.; Sunkara, Sirisha; Sparks, Andrew; Bai, Yun; Verratti, Kathleen; Saeed, Kelly; Venepally, Pratap; Jarrahi, Behnam; Fleischmann, Robert D.; Peterson, Scott N.

The GSEQ software produces a CHP file containing the base call, the corresponding reference base and a quality score for each locus on the resequencing chip. Our bioinformatic filters consist of a set of Perl scripts that operate on the CHP files and produce a list of highconfidence SNP calls from the larger raw set of SNP calls present in those files. The scripts are available for download from our website (http://pfgrc.jcvi.org/ presentations/data/snp_filter_scripts/snp_filter_scripts. shtml). Each filter serves to reduce the number of candidate SNPs. The output of one filtering step becomes the input for the next.