Flagging Blacklisted regions instead of deleting them.

Question

[akshitiz09]

Hi Guys,

I have some Cnvnator calls in vcf format and I have ENCODE blacklisted regions in a VCF and BED format. Is there a way we can flag the regions instead of deleting them? I know using BEDTOOLS we can use intersect to delete the regions but instead is there a way we can keep the regions and just indicate in a way that these are blacklisted regions?

Any help will be appreciated. Thank you

Best, Rayz

[seidel]

I don't know the answer, but am wondering if you can use the INFO column of the VCF to add a key=value pair indicating that the variant is in a blacklist region. (?) (not really sure how much the INFO column is used for custom annotations).