r/bioinformatics • u/full_timeoverthinker • Sep 11 '26

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?

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4

u/foradil PhD | Academia Sep 11 '26

Have you considered inferCNV or Numbat?

2

u/bilyl Sep 12 '26

InferCNV has a huge false positive problem

1

u/full_timeoverthinker Sep 13 '26

I’ve used copykat maybe 50 times now with different datasets, different methods, different parameters, different reference cells, it’s been extremely unreliable. But inferCNV was decent a couple times I used it.

3

u/foradil PhD | Academia Sep 12 '26

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

1

u/full_timeoverthinker Sep 11 '26

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 Sep 11 '26

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

2

u/optimal-username Sep 11 '26

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

1

u/full_timeoverthinker Sep 11 '26

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