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Question: Problem with Annotation Regions using ANNOVAR Annotate VCF
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gravatar for meishiuekuo
6 months ago by
meishiuekuo • 0
meishiuekuo • 0 wrote:

Hello,

I'd like to use ANNOVAR Annotate VCF via Galaxy Web (Galaxy Version 0.2) to annotate variants of my VCF file. I need to put a value in "Annotation Regions" field. Whatever which value I put in, I got the same error messages saying that "Parameter regions requires a value, but has no legal values defined". After searching for a long time, I still don't have any idea what should be the legal values.

Many thanks for your help.
hg19 annotation snp vcf annovar • 440 views
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modified 6 months ago • written 6 months ago by meishiuekuo • 0
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gravatar for Jennifer Hillman Jackson
6 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Annovar at Galaxy Main https://usegalaxy.org has native indexes for the reference genome hg19 only. When given an input VCF with that database assignment, the options will populate.

Please note that this tool has a known issue with VCF output (tabular is fine). The earlier version (0.1) only outputs tabular data: https://github.com/galaxyproject/galaxy/issues/4001

Thanks, Jen, Galaxy team
ADD COMMENT • link written 6 months ago by Jennifer Hillman Jackson ♦ 25k
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gravatar for meishiuekuo
6 months ago by
meishiuekuo • 0
meishiuekuo • 0 wrote:

Thank you, Jennifer. I did use hg38 as reference genome to perform my analysis. This explains why Annovar at Galaxy didn't work. I'll try hg19 as reference genome and hope this will work.
ADD COMMENT • link written 6 months ago by meishiuekuo • 0
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