Hello, I end up using a lot more VariantAnnotator from GATK to treat my VCF files against anything I really want. I gave up using vcf-annotate, it's not very functional...
Right now I'm annotating using 1000genomes(nov2011), dbsnp135, Exome Variation Server, snpeff. And after this I also created a python script to include some annotations made with annovar (SIFT and Polyphen for example)
My big command:
command = "java -Xmx4G -jar ~/lgc/programs/GenomeAnalysisTK-1.4-30-gf2ef8d1/Geno
-E exome_server.MAF" % (options.vcf_file, options.vcf_file, filename)
It's very useful specially when we are receiving VCF Files from different centers and I want to include the same annotations that we use in house.