In particular, NGS technologies have been recently applied with great success to the discovery of muta-tions associated with the growth of various tumors and in rare Mendelian diseases. The advance in NGS technologies has also created significant challenges in bioinformatics. One of the major challenges is quali-ty control of the sequencing data. In this review, we discuss the proper quality control procedures and pa-rameters for Illumina technology based human DNA re-sequencing at three different stages of sequencing: raw data, alignment, and variant calling. Monitoring quality control metrics at each of the three stages of NGS data provides unique and independent evaluations of data quality from differing perspectives. Properly conducting quality control protocols at all three stages and correctly interpreting the quality con-trol results are crucial to ensure a successful and meaningful study.
The detailed QC strategies can be found in the manuscript.