Related to snpEff

Hi @Sheila / @Geraldine_VdAuwera / team :)

I would like to ask some question regarding to the snpEff using the input from GATK pipeline.

A really fast intro about what we are doing;
We currently in the stage of variant calling step using GATK for our whole genome human samples. From the vcf file produced, we run the snpEff. Out of 43 samples, there are several samples that weirdly came out.

The weird thing happen is that when the output from the snpEff showed that the "Number of known variants: 0"

Is there any problems with our vcf input file or anything else that we are lacking of?

Second question is, are we on the right path when we use hg19 package as the reference for annotation, alignment and variant call but we use the GRCh37.74 version for snpEff?

Thank you very much for your help. We must really appreciate it.



Issue · Github
by Sheila

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Best Answer


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi @Azlin,

    Since SnpEff is not our software, we're not equipped to diagnose issues that occur when running that program. One thing you can try is to run ValidateVariants to check whether your files are healthy. If that doesn't show the source of the problem, you'll need to ask the developers of SnpEff for help.

    We don't recommend mixing reference resource packages -- it's much safer to run everything with resources derived from the same reference.

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