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PGx in Estonia

75 bytes added, 13:15, 23 August 2018
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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), Genome STRiP (CNV calls for CYP2D6, 2269 patients), Astrolabe (allele matching for CYP2D6, for comparison) || 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), BWA-MEM (GRCh37 reference genome), Picard (mark PCR duplicates), GATK 3.4, bcftools (normalization and decomposition) || Otherwise same bioinformatic pipeline as WGS
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