Additional file 2.
Comparison of effect of marking duplication, realignment and recalibration. A detailed comparison of results using different steps, marking duplication, realignment and recalibration, in terms of dbSNP rate, Ti/Tv ratio, novel Ti/Tv ratio and NRD for all regions, inside target regions, outside ≤ 200 bp regions, and outside > 200 bp regions from Illumina whole-exome sequencing data. Initial alignment (black), marking duplication (yellow), realignment (violet), recalibration (blue), marking duplication followed by realignment (red), marking duplication followed by realignment and recalibration (brown).
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Liu et al. BMC Genomics 2012 13(Suppl 8):S8 doi:10.1186/1471-2164-13-S8-S8