bcftools AA annotation failing

Question

[Whirlingdaf]

I am attempting to annotate a phased vcf file with ancestral alleles (AA), but it is not working.

My original vcf file (less the full header) format is:

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  Sample1  Sample2    ...
chr1    2602    .       C       A       .       .       AC=0;AF=0.0155039;CM=0;AN=22    GT      0|0   0|0      0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0
chr1    2614    .       G       A       .       .       AC=0;AF=0.0193798;CM=1.2e-05;AN=22      GT    0|0      0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0

My annotation file with the AAs I would like to bring over into the original vcf is:

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO
chr1    2602    .       .       .       .       .       AA=C
chr1    2614    .       .       .       .       .       AA=G
chr1    2649    .       .       .       .       .       AA=C
chr1    2830    .       .       .       .       .       AA=G

Here is the bcftools command:

bcftools annotate -a ancestral_alleles.vcf.gz -c CHROM,POS,INFO/AA -h hdr.txt -o annotated_ancestral.vcf original.vcf.gz

The output vcf file header includes:

##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##fileDate=07/08/2024 - 01:30:48
##source=shapeit4.1.3
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency">
##INFO=<ID=AC,Number=1,Type=Integer,Description="Allele count">
##INFO=<ID=CM,Number=A,Type=Float,Description="Interpolated cM position">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Phased genotypes">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele">
##bcftools_annotateVersion=1.19+htslib-1.19.1

While the file looks like:

chr1    2602    .       C       A       .       .       AC=0;AF=0.0155039;CM=0;AN=22    GT      0|0     0|0     0|0     0|0     0|0     0|0     0|0       0|0     0|0     0|0     0|0
chr1    2614    .       G       A       .       .       AC=0;AF=0.0193798;CM=1.2e-05;AN=22      GT      0|0     0|0     0|0     0|0     0|0     0|0       0|0     0|0     0|0     0|0     0|0

But I would like it to look something like:

chr1    2602    .       C       A       .       .       AC=0;AF=0.0155039;CM=0;AN=22;AA=C    GT      0|0     0|0     0|0     0|0     0|0     0|0     0|0       0|0     0|0     0|0     0|0
chr1    2614    .       G       A       .       .       AC=0;AF=0.0193798;CM=1.2e-05;AN=22;AA=G     GT      0|0     0|0     0|0     0|0     0|0     0|0       0|0     0|0     0|0     0|0     0|0

[Pierre Lindenbaum]

I suppose it's not working because when you use a vcf as an annotation source, the REF (and ALT ?) allele is required ?

just try again but add the REF/ALT for the two variants above, just to check if that works.

[Whirlingdaf]

Ah! Maybe you are on to something. Do you expect this would probably also be the case for a tab separated (bgziped and indexed) file as well? E.g.:

chr1    2602    C
chr1    2614    G
chr1    2649    C
chr1    2830    G

[Pierre Lindenbaum]

yes, a tab instead of a vcf should work.

[Whirlingdaf]

Thank you so much, yes, this worked!