WES CNV analysis

Question

[Avinash]

Hi,

I am new to CNV analysis and beginner in R language. I am trying to call germline CNVs using exome data using ExomeDepth. I only have the raw data with hg38 reference.

If you have the ExomeDepth scripts to run on hg38 reference. Kindly share me the scripts. It would be a great help for me to continue the analysis. Also share me the hg19 current script that you are without any bugs.

I have tried CNVkit but it was less accurate in detecting CNVs smaller than 1 Mbp but my samples are mostly less than 1Mbp duplication or deletion. So I tried to shift with other tools ExomeDepth, Conifer, GATK gCNV, CONTRA etc. If you have any successful tools that works well fits for my scenario. Kindly suggest me.

Thanks in advance.

Avinash

[Pierre Lindenbaum]

f you have the ExomeDepth scripts to run on hg38 reference. Kindly share me the scripts.

https://github.com/search?q=ExomeDepth+path%3A*.sh&ref=opensearch&type=code

https://github.com/search?q=ExomeDepth+path%3ASnakefile&ref=opensearch&type=code

https://github.com/search?q=ExomeDepth+path%3A*.nf&ref=opensearch&type=code

....

without any bugs

I don't make mistakes. I create teachable moments.

— Shit Academics Say (@AcademicsSay) March 12, 2016

[Avinash]

Hi,

Thank you so much for your help. I will try to run ExomeDepth along with some other CNV tools.

Kindly suggest me some other WES CNV tools

Yeah definitely I will create teachable moments!