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The Estonian Genome Centre at the University of Tartu has done a considerable job with [https://doi.org/10.1101/356204 Translating genotype data of 44,000 biobank participants into clinical pharmacogenetic recommendations].
We here list the bioinformatic pipelines used for the biobank
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! Technology !! Methods !! Comments
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| High density microarrays || HumanOmniExpress beadchip (OMNI, 8132 patients) and Global Screening Array (GSA, Illumina, 33157 patients), GenomeStudio (Illumina, genotyping, filtering for GSA), PLINK (filtering for all), zCall (genotyping rare variants for GSA) || 1308 of these patients were also Whole genome sequenced
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| Whole genome sequencing || TruSeq PCR-free prep, Illumina HiSeq X (150bp paired-end, 30x mean coverage), BWA-MEM (GRCh37 reference genome), Picard (mark PCR duplicates), GATK 3.4, bcftools (normalization and decomposition) || Quality filtering parameters are given in the article. The WGS samples (with some modifications) were also merged into a reference panel used for imputation (total 2279 Estonians and 1856 Finns)
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| Whole exome sequencing || Agilent SureSelect Human All Exon V5+UTRs target capture kit, HiSeq2500 (67x mean coverage) || Otherwise same bioinformatic pipeline as WGS
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We here list some of the challenges and solutions they identified:
