Question regarding CODEX2 results

[Thomas Jones]

Dear Yuchao, 

I hope you are well and thanks again for your previous help. I have a question regarding some of the results I have found consistently when running CODEX2, any input would be appreciated. 

As recommended, I load my results into IGV and look for regions where common CNVs are found. An example of which is shown below, gnomAD reports this CNV, but only as a common deletion. I have several results like this where I call expected deletions at the expected frequency but also find a number of unexpected duplications in the same region (and vice versa). I was wondering if you encounter this problem and if you have any recommendations to overcome this? 

Many thanks,

Tom Jones

The Francis Crick Institute Limited is a registered charity in England and Wales no. 1140062 and a company registered in England and Wales no. 06885462, with its registered office at 1 Midland Road London NW1 1AT

[Jiang, Yuchao]

Hi Tom,

Thanks for your interest. Can you let me know how you set up the CODEX2 run? Do you have negative control samples and/or negative control regions? How did you identify the regions to force call? Is it through a first pass CODEX2 run or manually input?

Additionally, have you tried to visualize the results from https://htmlpreview.github.io/?https://github.com/yuchaojiang/CODEX2/blob/master/demo/CODEX2.html#running-codex2-without-specifying-negative-control-samplesregions ? Usually this one is much more stable than force calling with only negative control regions.

Yuchao

On Aug 20, 2020, at 8:10 AM, Thomas Jones <thomas...@crick.ac.uk> wrote:

Dear Yuchao, 

I hope you are well and thanks again for your previous help. I have a question regarding some of the results I have found consistently when running CODEX2, any input would be appreciated. 

As recommended, I load my results into IGV and look for regions where common CNVs are found. An example of which is shown below, gnomAD reports this CNV, but only as a common deletion. I have several results like this where I call expected deletions at the expected frequency but also find a number of unexpected duplications in the same region (and vice versa). I was wondering if you encounter this problem and if you have any recommendations to overcome this? 

<image.png>

Many thanks,

Tom Jones

The Francis Crick Institute Limited is a registered charity in England and Wales no. 1140062 and a company registered in England and Wales no. 06885462, with its registered office at 1 Midland Road London NW1 1AT

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