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Convert GVF to VCF
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2.1 years ago
win • 810
India

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,

vcf • 2.7k views
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16 months ago
Ying W ♦ 3.9k
South San Francisco, CA

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

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thanks, just what i was looking for.

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2.7 years ago
dwaggott • 270
United States

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

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

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