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Why is Variant Annotator not annotating homozygous reference SNPs??

iolaldeiolalde Member
edited February 2013 in Ask the GATK team

Hi, I'm using The Genome Analysis Toolkit (GATK)-1.6-11.
I generated a VCF file using Unified Genotyper, option EMIT_ALL_CONFIDENT_SITES. Now I want to annotate the ID field with the rs identifiers from dbSNP. When I run Variant Annotator :

-T VariantAnnotator -R ref.fasta --variant variants.vcf --dbsnp dbsnp.vcf --out variants.annotated.vcf

It only annotates SNPs that are heterozygous or homozygous for the alternative allele, but not the ones that are homozygous for the reference allele.

I guess it has something to do with the ALT field, which has a dot in homozygous reference SNPs.
Thanks in advance,



  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi Iñigo,

    You're using an older version of GATK for which we can't provide support. Could you please update to the latest version and try again?

    FYI the dot in the ALT field just means that there is no alt allele, and is expected for hom-ref calls.

  • egafniegafni Member

    This is also happening with GATK2.5 with most annotations. For example, homozygous reference sites aren't being annotated with FS, HaplotypeScore or ABHom. Some annotations like BaseCounts work.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Many annotations are not applicable to homozygous reference sites. We're try to make that clearer in the documentation.

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