Table 1.

Troubleshooting table.

Step	Problem	Possible reason	Solution
14	Error message: “Memory allocation failed!”	Insufficient computing memory	Rerun the script on a high-memory machine. Alternatively, use a less memory-intensive, successfully implemented strategy for identifying SUNKs detailed in our study of patients having the 17q21.31 microdeletion syndrome14.
67	Fluorescence curves for non-water reactions do not all plateau around the same value	DNA concentrations of samples used were not all within a narrow range	Measure the concentrations of samples used. If they are not all within a narrow range (within a few ng/μl), dilute the samples so that they come to be all within a few ng/μl of each other and perform the MIP capture and exonuclease treatment again with these samples.
95	Smaller band present in addition to band ~288 bp in size	Significant amount of smaller amplicons in PCR reaction products	Perform the cleanup steps again using a smaller ratio than 1.8 (as low as 0.6) for the volume of magnetic beads added per microliter of pooled PCR reaction product. Perform size confirmation by gel electrophoresis to ensure that having followed the modified cleanup protocol effectively removed the smaller band from the final library for sequencing.