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
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
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
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.
