SNP microarray concordance with known genotypes before and after local re-alignment of U87MG. SRMA was applied to the alignments produced with BFAST of a human cancer cell line (U87MG; SRA009912.1). Heterozygous genotypes from an Illumina SNP microarray were compared with genotypes called from sequence data before and after application of SRMA (see Materials and methods). A minimum threshold on three different variant-calling metrics was applied, respectively, to improve the concordance (y-axis) while reducing the total number of SNP positions on the microarray that were called. Regardless of the metric, SRMA reduced the discordance (one minus concordance) of heterozygous SNPs reported by the SNP microarray and sequencing data.
Homer and Nelson Genome Biology 2010 11:R99 doi:10.1186/gb-2010-11-10-r99