I am trying to annotate a VCF file by adding DBSNP information to the INFO column, using the given below annotation file
CHROM FROM INFO/DBSNP 1 69428 dbSNP_134 1 69476 dbSNP_134 1 69496 dbSNP_134 1 69511 dbSNP_131 1 69590 dbSNP_134 1 69594 dbSNP_134
Both the VCF file and annotation file was bgzipped and tabix indexed. Used the following vcftools vcf-annotate command for it
zcat sample.vcf.gz | vcf-annotate -a annotation.txt.gz -d key=INFO,ID=DBSNP,Number=1,Type=String,Description='My annotation' -c CHROM,FROM,INFO/DBSNP >test_annotated.vcf
The command ran without any errors creating the output VCF file named 'test_annotated.vcf' with just a header line with description of INFO/DBSNP added to it, but DBSNP information was not added to any variants. Both the VCF and Annotation file have variants with CHR and POS in common too. Not sure why it is not getting annotated.
Has anyone successfully done this before. Any help is much appreciated. I posted the same question over at VCFtools-help http://bit.ly/ZjT3YG Petr or Adam, appreciate some help :)