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NGS
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* Short read NGS requires a priori knowledge of likelihood of particular haplotypes. ''In silico'' haplotype estimation can e.g. be performed by [http://faculty.washington.edu/browning/beagle/beagle.html Beagle].
* Variants in homologous regions are hard to capture.
* HLA-typing require special software, e.g. [https://software.broadinstitute.org/cancer/cga/polysolver Polysolver] for whole exome sequencing or [https://github.com/FRED-2/OptiType OptiType] for whole genome sequencing
