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Why is Variant Annotator not annotating homozygous reference SNPs??
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,