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etal / cnvkit

Copy number variant detection from targeted DNA sequencing
http://cnvkit.readthedocs.org
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How to get raw vcf without filtering CNV events? #698

Open xiucz opened 2 years ago

xiucz commented 2 years ago

Hi, @etal

How to get the raw vcf without filtering any lines using cnvkit.py export vcf?

Best, xiucz

etal commented 2 years ago

It's not an option for VCF. But it is an option for BED format: cnvkit.py export bed --show all. Will that format work for your pipeline?

xiucz commented 2 years ago

Now , I think it is reasonable to filter in the VCF. But how about add the same --show all to the cnvkit.py export vcf commander line?