Re: On running CODEX2 with 1000genomes GRCh38 WES data.

[Jiang, Yuchao]

Hi,

It seems something is wrong in the previous steps, e.g., when you calculate the GC content etc.

Yuchao

On Dec 7, 2019, at 9:54 AM, Furkan Ozden <furkan...@bilkent.edu.tr> wrote:

Hello Mr. Jiang,

I am Furkan Ozden, a researcher from Bilkent University, Turkey. I have red your paper "CODEX2: full-spectrum copy number variation detection by high-throughput DNA sequencing”.

For research purposes we are trying to run CODEX2 on 1000genomes GRCh38 Exome Data. 

However in Quality Control step;

qcObj <- qc(Y, sampname, ref, cov_thresh = c(20, Inf),
	length_thresh = c(20, Inf), mapp_thresh = 0.9,
	gc_thresh = c(20, 80))

At this filtering step, we get the error of “NA number of exons are filtered due to extreme GC content” and the script stops working. 

Is it possible for you to share the results with us  if you have CODEX2 already run on this data in order to save time?

Thank you in advance,

Furkan Ozden,

Bilkent University Computer Science Dept., 

Ankara, Turkey