Skip to main content

Table 1 Chromosome 1 Bis-SNP detection

From: Bis-SNP: Combined DNA methylation and SNP calling for Bisulfite-seq data

Sample Aligner reference cvg Het SNPs Hom SNPs Callable bases runtime
OTB MAQ hg18 32× 119,103 67,725 211,042,010 2.8 h
TCGA-lung-normal BSMAP hg19 19× 118,412 58,309 222,763,786 3.1 h
TCGA-breast-normal BSMAP hg19 19× 113,009 57,281 221,014,965 2.7 h
Mouse-F1i Novoalign mm9 50× 663,528 65,364 178,718,615 3.1 h
Mouse-F1r Novoalign mm9 41× 682,979 67,068 178,847,508 3.1 h
  1. Notes: All benchmarking performed using a single Intel(R) Xeon (X5650,2.67 GHz) server with 12 CPU cores and 10 GB memory. SE refers to single-end sequencing and PE to paired-end.