Cross-sample contamination check

Cross-sample DNA contamination is performed using software verifyBamID2 integrated into the automated pipeline. Samples with >1.5% contamination will pause the pipeline. This is then investigated and, if appropriate, the residual sample is re-sequenced and run through the pipeline. If there is a repeated failure then a sample failure report is generated. More details can be found in the Data QC issues section of the Unhappy Paths SOP.