SliderII Results of SNPs concordance comparison to Maq.We used 68 lanes human whole genome shotgun sequencing, WGSS, PET data (real data), a total of 906 million reads sizes from 36 to 42 bases, using each of SliderII and MAQ, we aligned these reads to the human genome hg18 resulting a coverage of about 7.5 X. For each aligner, SNPs are sorted in descending order, using SNPs score for SliderII, and the Phred-like consensus quality score for MAQ. Concordance with Ensembl Variation 50 SNPs is used to compare SNPs calling accuracy.
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Malhis et. al. 2008
High Quality Alignment and SNP Calling for Illumina High Throughput Sequence Data
Bioinformatics (2009) 25 (1): 6-13