chenweng1991
commented
4 months ago Dear @chilampoon Thank you for your question and your interest. In the redeemR package the function Create_redeemR and Vfilter_v4 are the two major function together doing the filtering. The source code are in the folder of R/BuildTree.R Perhaps you can check if you have filtered by maxctscut=2 which is to only take variants that have at least 2 or more than 2 molecules per cell in at least one cell. This is a filtering to remove potential NUMT influence. But please check the source code as well. Please feel free to let me know if you have any other questions.
Best regards --Chen
hello there! thanks for making all the packages and notebooks. I was looking at the mtSNVs in one of the rds files downloaded from here https://doi.org/10.6084/m9.figshare.23290004 and trying to do the same filtering as described in the nature paper. However after my filtering there are ~ 43k mismatches left, a number much higher than what you stated in the paper (~3 or 4k mt mutations). Could you please point me to the actual code or maybe a more specific description about how you processed the mutation calls? thank you very much!