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 Affymetrix GeneChip Õ Sequence Analysis Software (GSEQ) Version 4.0 was used to analyze hybridization results and to obtain raw data. The GSEQ software implements a batch analysis approach that allows correction for background signals by comparing signal intensities at each base position across a set of samples that makes up a batch. We used a batch size of 16. Fifteen samples were selected to maximize sample diversity and establish a background set. Each query sample was added individually to the batch for analysis. Sample diversity was determined by phylogenetic analysis (Supplementary Figure 2 ) using the resequencing results from 40 samples analyzed in non-batch mode. Except when noted, we used the following analysis parameters in the GSEQ software: default setting for filter conditions, haploid genome model, trace threshold and sequence profile threshold in final reliability rules was used. The quality score threshold was set to 12.000 in the base-calling parameters and the call rate cutoff across samples was turned off (0.0000). 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.