how to deal with "too many missing data"

[jeffchen2000]

Hi BnpC support

from your published paper, your tools are best to deal with missing data (more than 20% missing).

Now. we have targeted sequencing snDNA samples from FFPE, with has lots of missing data due to the random fragmentation of DNA. (By the way, we cannot use regular filter thresholds to reduce the % missing data, otherwise, we will not get any cells). With such large % missing data (~50%), we got too many singleton clusters (which certainly not make sense). now what are the best parameters settings to avoid such a issue?