I have a VEP annotated VCF files with CADD and LOFTEE annotations. I need to filter in results with either CADD score >= 20 OR LOFTEE HC without any flag
My code is as following
filter_vep -i VEP_annotated.vcf -o VEP_filtered.vcf --format vcf --force_overwrite --filter "CADD_PHRED >= 20 or (LoF = HC and LoF_filter = . and LoF_flags = .)"
I guess the problem is that "LoF_filter" and "LoF_flags" should be blank (no value) but I am not sure how I should express this in the code (I tried = "" but still not working)?
Thank you very much