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Changes
NGS
,→Challenges
==Challenges==
* Short CNV and other haplotype calling is challenging due to short read . NGS requires a priori knowledge of likelihood of particular haplotypes. ''In in silico'' CNV and haplotype estimation . Haplotype calling can e.g. be performed by [http://faculty.washington.edu/browning/beagle/beagle.html Beagle].
* Variants in homologous regions are hard to capture. Notably, the genes CYP2D6 and CYP2A6 are challenging.
* HLA-typing require special software, e.g. [https://software.broadinstitute.org/cancer/cga/polysolver Polysolver] for whole exome sequencing (WES) or [https://github.com/FRED-2/OptiType OptiType] for whole genome sequencing (WGS)
