If I run a custom panel using a subset of the amplicons in the Tapestri Genome-Wide CNV Panel, can I use the Genome Integrity pipeline to analyze my data?

Yes, please use your custom panel files in place of the gwCNV panel files. When designing your custom panel, please consider that the median ploidy captured is assumed to be diploid. Therefore, over 50% of the amplicons in your panel should be designed to target predicted diploid regions.