Creating bed file for gene specific variant extraction from VCF file

Question

[karthick.n]

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

Answer 1

[Amitm]

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

[karthick.n]

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

Regards, Karthick

[karthick.n]

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

[Amitm]

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.