* CNV and other haplotype Bad coverage of pharmacogenes. Notably, the lack of intronic variants in WES.* Haplotype calling is challenging due to short readreads. NGS requires ''in silico'' CNV and haplotype estimation. Since GATK 3.3, the [https://software.broadinstitute.org/gatk/documentation/tooldocs/3.8-0/org_broadinstitute_gatk_tools_walkers_haplotypecaller_HaplotypeCaller.php Haplotype calling Caller] assemble contigs of 300 base pairs, but it does not consider the phasing of the reads. Haplotype phasing can e.g. be performed obtained by Trio analysis, or estimated by imputation methods [http://faculty.washington.edu/browning/beagle/beagle.html Beagle]or [http://dx.doi.org/10.1038/ng.3679 Eagle2] or [https://doi.org/10.1371/journal.pgen.1004234 SHAPEIT]. Other possible options at Oslo University Hospital are long read technology from [https://www.sequencing.uio.no/services/pacbio.html PacBio] or synthetic long reads from [https://www.sequencing.uio.no/news/2019/10x%20Genomics%20is%20here%21 10x Genomics]* Variants Difficult variant calling in homologous regions are hard , such as CYP2D6. I.e. regions with copy number variations (CNV) or pseudogenes. The CYP2D6 genotyping tool that was used by [https://github.com/PharmGKB/PharmCAT/wiki PharmCAT] is [https://www.nature.com/articles/npjgenmed201639 Astrolabe]. We intend to captureuse the more recent program [https://github. Notably, the genes CYP2D6 and CYP2A6 are challengingcom/inumanag/aldy Aldy].* HLA-typing require special software, e.gThere are many options. [https://doi.org/10.1002/cpt.411 Yang et al. ] proposed to use [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). [https://doi.org/10.1101/356204 Reisberg et al.] proposed [https://doi.org/10.1371/journal.pone.0064683 SNP2HLA] for WGS. The candidate that we are investigating closer is [https://github.com/humanlongevity/HLA xHLA]. * New variants are discovered, and needs to be [[gene function|functionally assessed]].

[[PGx in Estonia|Solutions A solution for PGx on NGS genotyping biobank data]] are given has been investigated by ''Reisberg et al.'' in their article [https://doi.org/10.1101/356204 Translating genotype data of 44,000 biobank participants into clinical pharmacogenetic recommendations: challenges and solutions].

An excellent solution for genotyping a collection of ADME (absorption, distribution, metabolism and elimination) genes for individual patients is Aldy, which is fast, accurate and relatively simple to use. ==PublicationsInteresting publications==

| University of Tartu || [https://doi.org/10.1101/356204 Translating genotype data of 44,000 biobank participants into clinical pharmacogenetic recommendations: challenges and solutions] || Well-described pipeline for PGx on biobank data. WES cannot be used for PGx (important variants missing, imputation and CNV calling difficult)