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
meAnalysisTK.jar
-T VariantAnnotator
-R ~/lgc/datasets/gatk_data/b37/human_g1k_v37.fasta
-A SnpEff
--variant %s
--snpEffFile snpEff_output.vcf
-L %s
-o %s.snpeff.dbsnp135.exomeserver.vcf
--dbsnp /home/raony/lgc/datasets/dbsnp/dbsnp-135.vcf
--resource:dbsnp135 /lgc/datasets/dbsnp/dbsnp-135.vcf
--resource:exome_server /lgc/datasets/exome_variation_server/ESP5400.snps.vcf
--resource:1000genomes /lgc/datasets/1000new_release/ALL.wgs.phase1_release_v2.20101123.snps_indels_sv.sites.vcf
-E 1000genomes.AF
-E dbsnp135.GMAF
-E dbsnp135.dbSNPBuildID
-E exome_server.AAC
-E exome_server.GS
-E exome_server.PP
-E exome_server.CDP
-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.
what is your 'VCFtools' ? I cannot see a 'vcf-annotate' in http://vcftools.sourceforge.net/options.html
Which version of VCFtools did you use, remeber to always mention the version!