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Error from snpEff annotate

Hi all,

It is my first time to use snpEff to annotate my VCF file generated from GATK. After software installation and reference genome download, I use the typical command to do annotation as below.

java -jar SnpSift.jar annotate referenceVCFfile.vcf myVCFfile.vcf > variants_annotated.vcf

The first error came out, 

**Error        :    Unknown parameter 'myVCFfile.vcf'**.

Could you share the solutions or advice?
Thanks.

snpeff annotate
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updated by Ram Ram • written by boymin2020 • boymin2020

Hello boymin2020!

We believe that this post does not fit the main topic of this site.

check my question

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written by boymin2020 • boymin2020

Hello,

what version are you using? What happens if you start java -jar SnpSift.jar annotate without any parameter?

fin swimmer

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written by finswimmer finswimmer

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