Convert GVF to VCF

Question

[win]

Hi all.

Does any know of a script or code that can convert a GVF file to VCF? There is a reference to a link https://code.google.com/p/gvf2vcf/ but it is not accessible anymore.

Any help will be appreciated.

Thanks

Answer 1

[Ying W]

Found a perl script here that should do it (scroll to bottom for usage instructions)

[Dan]

Here is the canonical version of the script: https://github.com/Ensembl/ensembl-variation/blob/master/scripts/misc/gvf2vcf.pl

[george-hall-ucl]

This has moved - it is now at: https://github.com/Ensembl/ensembl-variation/blob/main/scripts/misc/release/gvf2vcf.pl.

[win]

thanks, just what i was looking for.

Answer 2

[dwaggott]

Try installing gvcftools. I got it to work recently.

zcat tmp.gvcf.gz  | break_blocks --region-file clinvar.bed --exclude-off-target --ref  ucsc.hg19.fa | bcftools view -O z >  tmp.vcf.gz

Also, bcftools is starting to support it.

https://github.com/samtools/bcftools/issues/151

[win]

I was looking to convert GVF file into VCF not a gVCF file (genome VCF file). Any idea?

Answer 3

[Alireza]

Also, The following script works well for this purpose.

https://github.com/Test-Blu/GVF2VCF_Convertor_TestBlu