Integrated quality control across assays by evaluating concordance of genetic variants between SNP genotyping, RNA-seq and ATAC-seq. A simple approach would be to directly call genetic variants from RNA-seq and ATAC-seq and compare across assays. Since variant calling from functional genomics assays is technically challenging and has a high error rate, we used a statistical method to compare a BAM file from RNA-seq and ATAC-seq to the SNP genotyping data and evaluate the read support for each sample using only autosomes. BAM files using reads aligned to GRCh38 were compared to genotype data originally processed on GRCh37, but subsequently lifted overt to GRCh38. VerifyBamID48 was used to match RNA-seq data to SNP genotyping. Using the flags --best--ignoreRG--verbose, we identified each RNA-seq sample’s best genotyping match, and removed potentially contaminated samples, as judged by the chipmix and freemix estimates. If a BAM file matched to the expected individual in the SNP genotype data, the sample was accepted if its chipmix and freemix parameters were both below 0.2 (Fig. 7). Higher values for chipmix and freemix can indicate contamination, so samples exceeding
