GATK4 CNV, output 3 million CNVs !!!

Hi, there:

I was very excited to know that GATK4 could now generate CNV data from WGS.

However, I spent long time to make it work, but I think it still does not.

I recently followed all the instructions and managed to generate an output file. But this file has almost 3 million rows. The first 15 rows of the output file is shown below.

I think each person is expected to have ~1,000 CNVs, not ~3 million!!!
I understand that GATK is using a 1KB sliding window to detect CNV. But then how could I get the ~1,000 CNVs that I could use to run downstream analyisis?

Your help would be greatly appreciated!

Thank you & best regards,
Jie