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