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Question: Annovar is returning a file with only headers
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gravatar for hina.sultana
10 weeks ago by
hina.sultana • 0
hina.sultana • 0 wrote:

Hi

I am trying to do some variant analysis. I have mapped the reads using hg19 as reference through BWA MEM and then performed variant calling by FreeBayes. Now I am trying to annotate the variants using ANNOVAR, but it is returning a file with only headers. This is my first time using ANNOVAR so may be I am making some mistake. I am not sure what I should select for gene annotations, annotation regions and annotation databases.

thank you
snp annovar • 86 views
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modified 10 weeks ago by Jennifer Hillman Jackson ♦ 25k • written 10 weeks ago by hina.sultana • 0
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gravatar for Jennifer Hillman Jackson
10 weeks ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hi,

It looks like you have worked out the usage for the tutorial and have results now. Hg19 is supported at Galaxy Main https://usegalaxy.org and at least one annotation needs to be selected, otherwise, there is nothing to compare/add to the VCF's SNPs.

Thanks! Jen, Galaxy team
ADD COMMENT • link written 10 weeks ago by Jennifer Hillman Jackson ♦ 25k
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