Turning Vice into Virtue: Using Batch-Effects to Detect Errors in Large Genomic Data Sets.

ABSTRACT: It is often unavoidable to combine data from different sequencing centers or sequencing platforms when compiling data sets with a large number of individuals. However, the different data are likely to contain specific systematic errors that will appear as SNPs. Here, we devise a method to detect systematic errors in combined data sets. To measure quality differences between individual genomes, we study pairs of variants that reside on different chromosomes and co-occur in individuals. The abundance of these pairs of variants in different genomes is then used to detect systematic errors due to batch effects. Applying our method to the 1000 Genomes data set, we find that coding regions are enriched for errors, where ∼1% of the higher frequency variants are predicted to be erroneous, whereas

SUBMITTER: Mafessoni F 

PROVIDER: S-EPMC6185451 | biostudies-literature | 2018 Oct

REPOSITORIES: biostudies-literature