snpEff database to annotate b37 GATK output
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4.4 years ago
DVA ▴ 570

Anyone uses SnpEff to annotate GATK output? After downloading the newest snpEff (03/29/2017), I found that there is only one database avaliable to annotate hg19/b37 data and that is GRCh37.75. My question is: would this database be appropriate for my GATK output, which was previously aligned/handled using b37 reference? If so, great. If not, I would appreciate your solutions and suggestions.

Of note, I understand that GATK nowadays recommend Oncotator, but that seems to be mainly for cancer research. I also understand that some old GATK posts (e.g. http://gatkforums.broadinstitute.org/gatk/discussion/6619/snpeff-and-variantannotator and http://gatkforums.broadinstitute.org/gatk/discussion/50/adding-genomic-) recommended an older version of snpEff. However, to my understanding, that is to have snpEff output compatible for GATK VariantAnnotator, and now since snpEff can output VCF, to use older version should be no longer necessary. (And even I go with an older version, can I actually find GRCh37.64? That was from year 2011). Please correct me if I'm wrong. Thank you.

snpeff gatk • 1.7k views
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IMHO, that should be fine.

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4.3 years ago
hns ▴ 150

you have nothing to worry! It should work with what you have already!

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