Missing Copy Number Information for Some Clusters in Subcluster Mode

[nicolognoato]

Hi,

I am using InferCNV in subcluster mode to compute the copy number profile for a set of samples. The tool generates several output files, including:

• HMM_CNV_predictions.HMMi6.leiden.hmm_mode-subclusters.Pnorm_0.5.pred_cnv_regions.dat, which, from what I understand, is essentially the segmentation file where each cluster has segmentation regions with the associated copy number value.
• 17_HMM_predHMMi6.leiden.hmm_mode-subclusters.cell_groupings, which provides the mapping of each cell in my sample to its respective cluster.

For each sample, i notice that some clusters present in the 17_HMM_predHMMi6.leiden.hmm_mode-subclusters.cell_groupings file are missing from the HMM_CNV_predictions.HMMi6.leiden.hmm_mode-subclusters.Pnorm_0.5.pred_cnv_regions.dat file. This means that for cells belonging to these missing clusters, I lose copy number profile information.
1- Am I using the correct output files to retrieve the full copy number segmentation information per cluster?
If not, which output file contains the complete copy number profile for all clusters in subcluster mode?
2- Is this behavior expected, or could there be an issue with the way copy number predictions are being generated for some clusters?
Thank you in advance for your help!

Best,
Nicolò.