| Popis: |
The search for loci linked to diseases or drug targets is being studied by genotyping variants. Missing variants can be imputed, but the standard filtration methods applied during quality control(QC) reduced their number for downstream analyses.There is no standard protocol to retain the maximum of variants with reliable quality. To counteract this loss, we first limited the stringency of MAF SNP pre-filtration (MAF-DS), which improved post-imputation metrics with the 1000 Genomes (inc. INFO based on allele frequencies). Second, our two-step post-filtration strategy (1)computes a confident MAF threshold (MAF-DH), (2)filters with the quality score >0.3 and gains ~18% of reliable markers compared to conservative methods (single-step INFO>0.8) and confidence vs. non-conservative methods (single-step INFO>0.3).During the pre-and post-filtration steps, the MAF and allele accuracies were validated against a public database for further QC.The protocol is also applicable to any study since the metric MAFs are adapted to the sample set. |
