Question: How to get rsid during the variant annotation using VEP (offline mode)
2
gravatar for seta
8 months ago by
seta1.3k
Sweden
seta1.3k wrote:

Dear all,

I've got a large list of variant as VCF format per chromosome (human), which annotated using VEP (release 98) as offline mode. But, I didn't get the corresponding rsid at the output. Could you please help me out how I can obtain the "rsid" during the annotation?

Thanks

annotation vep ensembl • 481 views
ADD COMMENTlink modified 8 months ago by Emily_Ensembl21k • written 8 months ago by seta1.3k
4
gravatar for Emily_Ensembl
8 months ago by
Emily_Ensembl21k
EMBL-EBI
Emily_Ensembl21k wrote:

--check_existing=1

Checks for the existence of known variants that are co-located with your input. By default the alleles are compared and variants on an allele-specific basis - to compare only coordinates, use --no_check_alleles.

Some databases may contain variants with unknown (null) alleles and these are included by default; to exclude them use --exclude_null_alleles.

See this page for more details.

Not used by default

ADD COMMENTlink modified 8 months ago by zx87549.6k • written 8 months ago by Emily_Ensembl21k

Thanks Emily; I annotated VCF file of chromosome 22 and the "Existing_variation" column of output is empty, so what's happened in your view?

ADD REPLYlink modified 8 months ago • written 8 months ago by seta1.3k

Please share exact code you used.

ADD REPLYlink written 8 months ago by ATpoint38k

Then maybe you have novel variants.

ADD REPLYlink written 8 months ago by Emily_Ensembl21k

it's my mistake; actually, I thought the "check_existing" is considered by VEP as default. Now, with adding this item, the issue was solved.

ADD REPLYlink written 8 months ago by seta1.3k

If issue is resolved, please accept as an answer.

ADD REPLYlink written 8 months ago by zx87549.6k
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