Tools for chromosomal aneuploidy detection
1
0
Entering edit mode
25 days ago
adarsh_pp ▴ 40

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

human-genetics aneuploidy NGS • 332 views
ADD COMMENT
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode
21 days ago

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

ADD COMMENT

Login before adding your answer.

Traffic: 1312 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6