I want to update the FILTER column of a VCF

Although the old FILTER column has one filter flag per row, the new FILTER column will have some rows with multiple filter flag values delimited by semicolon

ie:

FILTER

QCFLAG1

QCFLAG2

QCFLAG1;QCFLAG2

when I run bcftools annotate -a my_annot_file.txt -c CHROM,POS,FILTER my_vcf.vcf

I get error:

The FILTER is not defined in the header: QCFLAG1;QCFLAG2

I think the problem is that while QCFLAG1 and QCFLAG2 are defined separately in the header, bcftools thinks QCFLAG1;QCFLAG2 is one filter that should be defined in the header.

I tried the --force flag but get same error.

I know I can do this manually with UNIX utilities, but I am hoping there is an easier high level way with some vcf parsing tool. Any suggestions? Thank you.