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.

Similarly, the retention of false positives that lie near predicted SNP locations indicates that the footprint effect filter also can be further refined. The footprint effect filter also had a relatively large negative impact on true positives in the SCHU S4 results (see Table 3 ). One underlying assumption of the current filter is that, within a set of closely spaced SNP calls, the one with the highest quality score is most likely to be the genuine SNP. This assumption may be violated in some cases, resulting in both false-positive and false-negative SNP calls. Another weakness of the current filter is that when two SNP calls lie within 10 base positions of each other, only one of the calls can survive the filter. Perhaps the effectiveness of this filter can be improved by examining signal intensities directly, rather than relying solely on the quality values assigned by the GSEQ software.