Fig. 7
Assessing sample concordance using genetic variants. Estimating contamination using Chipmix (x-axis) and Freemix (y-axis) output from VerifyBamID, on RNA-seq and genotyping data for HBCC and MSSM-Penn-Pitt cohorts. Each point is an RNA-seq sample and is colored according to whether the sample was accepted, excluded or rescued. Box in lower left-hand corner indicates criteria for a sample to be accepted if samples match the expected individual. Box in lower right indicates samples that were rescued by re-labeling to the proper individual. We note that this figure included samples there were excluded because of other filters.
