Convert GVF to VCF

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

• 9,953 views • link

updated 2.3 years ago by george-hall-ucl •

• written 11.5 years ago by win

3 answers

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

• 0 views • link

written 11.5 years ago by Ying W

thanks, just what i was looking for.

• 0 views • link

written 11.5 years ago by win

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

• 1 views • link

written 10.1 years ago by Dan

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

• 0 views • link

written 2.3 years ago by george-hall-ucl •

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

• 0 views • link

updated 11.5 years ago by Ram

• written 11.5 years ago by dwaggott

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

• 0 views • link

written 11.5 years ago by win

Also, The following script works well for this purpose.

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

• 0 views • link

written 3.5 years ago by Alireza •

More posts like this

Find common entries between VCF and ClinVar VCF
written 8.5 years ago by win

hi all, i annotated a VCF file with ClinVar annotations and that worked fine. What I am interested to know is which entries in my …
VCF evaluation for reporting
written 8.5 years ago by win

hi all, just as we use FASTQC for quality control check on output FASTQ files, i wanted to know if there any such commonly used …
Individual chromosome SNP VCF
written 8.5 years ago by win

Hi all, i am looking for hg38 dbSNP VCF file but for each chromosome separately. I am unable to download the entire genome VCF file …
HapMap in VCF format
written 10.2 years ago by win

Is there a HapMap file in VCF format for use with GATK. I found a post that discusses about conversion etc. but I wanted to …
Microarray to VCF
written 11.3 years ago by win

Hi all, I am wondering if someone know how to convert a microarray file correctly to a VCF file. There is 23me.com microarray data convertor …
Generate GVF file from VCF file
written 11.6 years ago by win

I have a VCF file and I want to generate gVCF file from that. http://blog.kokocinski.net/index.php/gvf-format?blog=2 Does anyone know of a converter that convert a VCF …
Tool or Script to convert MAF file to VCF ?
written 11.7 years ago by ttom

Hi, Does anybody know of any script/tool which could convert a MAF file to VCF? https://wiki.nci.nih.gov/display/TCGA/Mutation+Annotation+Format+%28MAF%29+Specification?showChildren=false Thanks, Tinu
Convert to Forward strand
written 11.8 years ago by win

Hi all, is it possible to convert all VCF data to forward strand? Is there a script that can do that? Thanks again in advance.
Annotate A Vcf File
written 12.9 years ago by win

hi all, i was wondering if someone could help. i wanted to know which annotation programs for VCF file especially the online ones. any place …
How To Validate A Snp Calling Pipeline With A Test Bam File
written 13.5 years ago by win

Hi all, I have a pipeline that and we want to make sure it works correctly. While we can test the VCF file in several …