Analysis to detect and genotype sequence variants differed among variant types and the three projects, but all workflows shared four features: Discovery: alignment of sequence reads to the reference genome and identification of candidate sites or regions at which one or more samples differ from the reference sequence.Filtering: use of quality control measures to remove candidate sites that likely were false positives.Genotyping: estimation of the alleles present in each individual at variant sites or regions.Validation: assaying a subset of newly discovered variants using an independent technology, enabling the estimation of the false discovery rate. Independent data sources were used to estimate the accuracy of inferred genotypes.
