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GATK4 CNV, output 3 million CNVs !!!
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,