dbSNP concordance 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). Variants were called with SAMtools before and after application of SRMA (see Materials and methods). Deletions and insertions (indels) called within U87MG were compared with those indels reported in dbSNP (v129). An increasing minimum SNP quality filter was used to improve concordance (y-axis) while reducing the number of indels observed at dbSNP positions (x-axis). Using SRMA significantly reduced the discordance (one minus concordance) between observed indels at dbSNP positions.
Homer and Nelson Genome Biology 2010 11:R99 doi:10.1186/gb-2010-11-10-r99