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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.
(http://www.ncbi.nlm.nih.gov/dbvar/content/ftp_manifest/)
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!

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by Sheila

Issue Number
813
State
closed
Last Updated
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vdauwera

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