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Despite the fact that both Whole Exome Sequencing (WES) and Whole Genome Sequencing (WGS) have been widely used in biological studies and rare disease diagnosis, limitations of these techniques on insertion and deletion (INDEL calling are still not well characterized. INDELs, especially those disrupting protein-coding regions of the genome, have been strongly associated with human diseases. However, there are still many errors with INDEL variant calling, driven by library preparation, sequencing biases, and algorithm artifacts.
(Fang et al., 2014) Reducing INDEL calling errors in whole genome and exome sequencing data. Genome medicine.