How to set variant FILTER in a VCF file based on overlap with regions in a BED file?
I guess this should be possible using e.g. bcftools
But the bcftools filter command can't do this annotation direct.
Seems like I first need to annotate the overlap in an INFO field.
Is there a way to set the FILTER status of a variant in 1 single command (without adding an INFO field) based on overlap of the variant with a region in a BED file?
Using bcftools or any other tool?