296
edits
Changes
→Bioinformatic pipelines
| 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), [https://www.ncbi.nlm.nih.gov/pubmed/22843986 zCall] (genotyping rare variants for GSA), Eagle2 (phasing), Beagle (impuation, population specific imputation panel from WGS) || 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), 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). Cf. [https://www.nature.com/articles/ejhg201751 Mitt ''et al.'']
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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) ||
