Question: Creating bed file for gene specific variant extraction from VCF file
gravatar for karthick.n
5 months ago by
karthick.n10 wrote:


I need to extract variants from VCF file for ACMG genes. I tried to create bed file from UCSC browser. But the bed file contains many accession ids for a single gene. How to make a bed file which will contains only one accession ID for one gene?

Regards, Karthick

acmg vcf genome • 187 views
ADD COMMENTlink modified 5 months ago by Amitm2.1k • written 5 months ago by karthick.n10
gravatar for Amitm
5 months ago by
Amitm2.1k wrote:

Hi, That is because the annotation data is transcript-centric and hence multiple (transcript ID) accessions per gene. I do not know of any way to collapse the output to gene-level.

But, you could do that using Ensembl BioMart. Under the "Attributes" section (left-hand menu), for the "Features" section (right-hand main-panel), choose only Gene stable ID (and keep transcript stable ID un-checked). In the output section, check the "unique results only" option and the output would be gene-centric. e.g. output showing coordinates at gene level

ADD COMMENTlink written 5 months ago by Amitm2.1k

Thanks a lot for your input! I will try this one :)

Regards, Karthick

ADD REPLYlink modified 5 months ago • written 5 months ago by karthick.n10

Hi Amit,

I tried this option. But I couldn't find the details for GRCh37. GRCh38 is the only genome available there. I used GRCh37 for my vcf file. Can you please suggest something to resolve this?

Regards, Karthick

ADD REPLYlink written 5 months ago by karthick.n10

Hi Karthick, Of course GRCh38 is now the default on genome browsers, but you could access the '37' by clicking the View in archive site link at the very bottom right-hand side of Ensmbl page. Alternatively, this is the direct link. The BioMart that you would access there would have GRCh37 data.

ADD REPLYlink written 5 months ago by Amitm2.1k
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