Tools for chromosomal aneuploidy detection

Question

[adarsh_pp]

Hi,

I am developing a pipeline for detection of chromosomal aneupoloidy detection based on single sample.

I went through several CNV calling tools, but most of them require control samples and all are based on read depths.

Are there any tools which can work without control samples and read depths.

Please suggest some tools for both short reads and long reads. Most probably this pipeline will be developed for long-read data.

I have already tried: QDNAseq. But I am unable to understand how the log2 cut offs are selected.

Please suggest.

Thanks

[cmdcolin]

is there any reason why you do not like tools based on read depths?

Answer 1

[a.alnawfal.1992]

As far as I know, all the tools utilised control group to compute the z score for chromosomal aneuploidy. but is your goal detect chromosomal aneuploidy or CNVs?

here some tools that might help in detecting CNVs:

NanoVar

Sniffles2

Control-FREEC