Filtering the v4 Exome CNV VCF

Structural Variation
1

Hello,

I am filtering the v4 Exome CNV VCF to get the final list of 66,903 rare CNVs.
The original vcf file has 68,699 rows (variants), but when I filter it on the FILTER-column (keeping only “PASS”) I get 67,952 variants. I read in your blog post that:
“There were 1,049 sites that produced noisy normalized read-depth signals and were also masked.” Which is the number of variants I need to remove to get from 67,952 to your number of 66,903 rare CNVs.
My question is: on what variable do you filter to get down to 66,903?

Thank you in advance for your help!
Best regards,

Lea

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