bcftools annotate doesn't liftover fields from VCF with symbolic alleles if END in only one file. #2507
Description
Hi,
I'm using bcftools annotate -c INFO -a variant_calls.vcf.gz imputed.vcf.gz to liftover annotations from a variant-call VCF (with meaningful INFO tags) into an imputed VCF (exact same variants, but removes the original INFO tags with other tags). Critically, the two files have the exact same number and order of variants, and POS/ID/REF/ALT are untouched. This works well for SNPs and most SVs, but seems to ignore symbolic alleles. Adding --pair-logic any/all does then carry over all the INFO annotation for all variants, but not the other options like id even though the symbolic allele variant has a unique ID.
It seems like the issue is that the symbolic alleles have their END info stripped by imputation, so the variants are no longer matched, since one is ID/end_pos and the other is just ID.
I guess this is an extreme edge-case as it is complex and probably fragile to only append END if both files have END, otherwise don't use it for either. I guess the most elegant/ugly solution would be to strip/rename the END tag, merge INFOs, and then rename END or recalculate from POS+SVLEN.
The versions are
bcftools 1.23-3-g34a49760-dirty
Using htslib 1.23-9-gacc28ac1-dirty
Best,
Alex