bcftools annotate multi-allelic weird behavior

Reproduce the report with the two VCF examples and the shown bcftools annotate command, comparing the long multi-allelic ALT values with the version where the final allele is G. Start by locating the annotate allele-matching path and add a regression case for these inputs; done means the final two annotations remain 9 and 10 rather than both becoming 9.

Hi,

I have spotted a weird behaviour when annotating some multi-allelic variants with bcftools annotate (v1.9).

Let say I have an external vcf containing the annotations Annot1 and Annot2 for a multi-allelic of 10 alternate alleles :

##fileformat=VCFv4.2
##INFO=<ID=Annot1,Number=A,Type=Integer,Description="Annot1">
##INFO=<ID=Annot2,Number=A,Type=Integer,Description="Annot2">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
1	123456	.	C	CTA,CTATA,CTATATA,CTATATATA,CTATATATATA,CTATATATATATA,CTATATATATATATA,CTATATATATATATATA,CTATATATATATATATATA,CTATATATATATATATATA	.	.	Annot1=1,2,3,4,5,6,7,8,9,10;Annot2=1,2,3,4,5,6,7,8,9,10

This is the original vcf I want to annotate:

##fileformat=VCFv4.2
##contig=<ID=1,length=249250621,assembly=b37>
##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
1	123456	.	C	CTA,CTATA,CTATATA,CTATATATA,CTATATATATA,CTATATATATATA,CTATATATATATATA,CTATATATATATATATA,CTATATATATATATATATA,CTATATATATATATATATA	.	.	AC=1,2,3,4,5,6,7,8,9,10

I use then the command
bcftools annotate -a annotation.vcf.gz -c Annot1,Annot2 original.vcf.gz
and I obtain this

1	123456	.	C	CTA,CTATA,CTATATA,CTATATATA,CTATATATATA,CTATATATATATA,CTATATATATATATA,CTATATATATATATATA,CTATATATATATATATATA,CTATATATATATATATATA	.	.	AC=1,2,3,4,5,6,7,8,9,10;Annot1=1,2,3,4,5,6,7,8,9,9;Annot2=1,2,3,4,5,6,7,8,9,9

So that I have 2 "9" in my annotations instead of 9,10 for the last 2 alleles.

Surprisingly if I rename the last allele from CTATATATATATATATATA to G in both my annotations and original vcf files I obtain the right result :

1	123456	.	C	CTA,CTATA,CTATATA,CTATATATA,CTATATATATA,CTATATATATATA,CTATATATATATATA,CTATATATATATATATA,CTATATATATATATATATA,G	.	.	AC=1,2,3,4,5,6,7,8,9,10;Annot1=1,2,3,4,5,6,7,8,9,10;Annot2=1,2,3,4,5,6,7,8,9,10

Could you explain why the behavior of the annotation command changes regarding the allele name ?

Best,