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How to do variant annotation?
I have difficulty running VQSR and the error message thrown at me complained the .vcf files were not annotated. The vcf files I use include the raw vcf generated by HaplotypeCaller, and those I downloaded from GATK public ftp (including hapmap_3.3.hg19.vcf, 1000G_omni2.5.hg19.vcf , 1000G_phase1.snps.high_confidence.hg19.vcf, and dbsnp_137.hg19.vcf).
My question here is do I need to annotate those vcf files downloaded from GATK public FTP? if yes, how?
I was reading some old documents and learned that I could use snpEff to annotate the files, but the questions is how can I add QD, FS, DP for SNPs calling and MQRankSum & ReadPosRankSum) for Indels calling?? It seems to me that the current best practice does not even mention snpEff any more (http://www.broadinstitute.org/gatk/guide/topic?name=best-practices), does this mean snpEff is no longer needed? or I can use VariantAnnotator to annotate all the necessary vcf files?
I know I have lots of questions. Thanks for your reply.