I've run into a weird error and would like to figure out what's going on.
I'm annotating a VCF file from a library VCF file using
bcftools annotate. I'm picking
AF fields from the library VCF file, and annotating them as a modified tag. This works fine for
AF, but does not work for
AC. My command is:
bcftools annotate -a library.vcf.gz \ -c "INFO/LIB_AC:=INFO/AC" \ -h library.vcfheader \ -Ov input_vcf
When I substitute all
AC above with
AF above, annotations happen fine. For the same entry that the
AF annotation is seen,
AC is not annotated even though the library file has both
AF for that matching (CHROM,POS,ID,REF and ALT matching) entry.
What am I missing here? Does
bcftools crap out if the annotation sub-tag picked out is the first annotation sub-tag (aka doesn't have a
; in front)?
I'm using bcftools v1.6
EDIT: I ran a few more tests.
I tried another attribute (
AN) and it works fine. It's only
AC that doesn't. And when I don't do the mapping(not
-c INFO/LIB_AC:=INFO/AC, only
-c INFO/AC), the
AC rightly replaces the
AC in my VCF. It's just unable to work in the way specific above. Really specific, really weird.