Problem with findShmTrees

[PpGrApee]

Hi, I have another problem. When I reviewed the result files from exportShmTreesWithNodes, I noticed that regions with empty nucleotide sequences are treated as if the entire region is mutated. Additionally, some amino acid sequences containing * or _ were also included in the findShmTrees analysis, which caused these positions to be counted as mutation sites. This significantly inflated my average SHM value. I believe these sequences should be removed before running findShmTrees. How can I address this issue?

SHMtrees.txt

[PpGrApee]

Hello, sorry. I have another problem. I find * in Germline in the result files from exportShmTreesWithNodes. How can I deal with this tree? Thank you!

SHMtrees2.txt

[mizraelson]

Unfortunately we don't have a way to filter those out in the output. I would recommend just filtering those out manually. Non productive sequences are important for the SHM trees generation algorithm as they are still a part of the lineage.

[PpGrApee]

Ok, Thank you.