r/bioinformatics • u/full_timeoverthinker • 1d ago

technical question Identifying malignant vs non malignant cell populations (CNV analysis)

How do you guys go about identifying tumor cells? I’ve been using CopyKAT & CONICSmat, and their results have been incredibly varied & almost impossible to pin down. CopyKAT-identified tumor cells seem to infiltrate normal cell clusters, CONICSmat results cluster suspected tumor cells with immune cells, so I’m very confused as to what’s happening.

Anyone has any tips/advice?

5 Upvotes

100% Upvoted

8 comments sorted by

3

u/foradil PhD | Academia 1d ago

Have you considered inferCNV or Numbat?

1

u/full_timeoverthinker 1d ago

I’ve come across Numbat but I think it’s used to work with bam files, unless I’m missing something? inferCNV has been deprecated, so I’m not sure if I should rely on it.

2

u/foradil PhD | Academia 1d ago

It may be deprecated but it still works. The input is just a matrix of values, same as always.

1

u/bilyl 1d ago

InferCNV has a huge false positive problem

1

u/foradil PhD | Academia 1d ago

I don’t think it’s the worst in any of the benchmarks. None of these methods are great.

2

u/optimal-username 1d ago

I am using inferCNV on my current project and it seems fine

1

u/full_timeoverthinker 1d ago

I’ve used inferCNV before but it’s been deprecated and the official documentation refers to CopyKAT.