Test-drive the GATK tools and Best Practices pipelines on Terra

Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

How to convert GVF to VCF

I want to convert a GVF file to a VCF file. However, I have problem when I did the conversion of the file formats.
I have downloaded the structural variation data from NCBI dbVAR by assemblies.
I found that there was only GVF format available by assemblies of dbVAR. However, the IndelRealigner does not support the GVF file as an input file.

I have tried several methods to convert a GVF file to a VCF file.
I found that VariantsToVCF in GATK and VCFtools are not support GVF as input file.
So I tried the script 'gvf2vcf', which is a tool in Ensembl perl API (https://github.com/hxin/DisEnt/blob/master/disnet/common/lib/ensembl-api/ensembl-variation/scripts/misc/gvf2vcf.pl). But the program always connects to the Ensembl database when I do the file conversion, and I want to do the analysis locally.

Is there anyone can help me? A lot of appreciate!


Issue · Github
by Sheila

Issue Number
Last Updated
Closed By

Best Answer


Sign In or Register to comment.