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How to do variant annotation?

rcholicrcholic DenverMember

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.

Best Answer

Answers

  • tommycarstensentommycarstensen United KingdomMember ✭✭✭

    @pdexheimer, do you know, if I can I force GATK VariantRecalibrator to use "functional annotations" manually added by me?

  • pdexheimerpdexheimer Member ✭✭✭✭

    @tommycarstensen, you could certainly add functional annotations for use by VariantAnnotator. Depending on what functional annotations you want, it may not be a simple annotator to add. Back in the old days (circa version 1.2) there was a VA module that added synonymous/non-synonymous annotations, but GSA dropped it. I think it was one of those that worked really well 95% of the time, but the bad 5% was a mess...

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    VariantRecalibrator can use any INFO field annotation that is appropriately defined in the header. The tricky part can be annotating your variants, which you can do by writing a custom annotator module, or with any other program that adds annotations to VCFs. Just keep in mind that the recalibrator expects some kind of numeric values, and assumes that the values are gaussianly distributed in your callset.

  • pdexheimerpdexheimer Member ✭✭✭✭

    I must have read that six times, and never once saw that it said "Recalibrator". Sorry about that...

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