Question: Is a custom Cell Ranger DNA contig-defs.json file required when analyzing cells with a baseline ploidy other than 2?
Answer: The contig-defs.json file stores information about the reference genome used during Cell Ranger DNA copy number variation analysis. This includes the
sex_chromosomes block, where the expected ploidy of the sex chromosomes is encoded:
These fields are meant to provide the normal baseline for the organism. Changes relative to the normal baseline will be reflected in the CNV calls. Therefore, no changes are necessary when analyzing cells that are expected to have consistent chromosomal abnormalities, such as XXY, XYY, trisomy 21, etc.
In fact, the pipeline does not currently use this information, which is present for forward compatibility.