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Question: Creating bed file for gene specific variant extraction from VCF file
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gravatar for karthick.n
5 months ago by
karthick.n • 10
karthick.n • 10 wrote:

Hi,

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
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modified 5 months ago by Amitm • 2.1k • written 5 months ago by karthick.n • 10
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gravatar for Amitm
5 months ago by
Amitm • 2.1k
UK
Amitm • 2.1k 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 COMMENT • link written 5 months ago by Amitm • 2.1k

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

Regards, Karthick

ADD REPLY • link modified 5 months ago • written 5 months ago by karthick.n • 10

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 REPLY • link written 5 months ago by karthick.n • 10

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 REPLY • link written 5 months ago by Amitm • 2.1k
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