Convert GVF to VCF
3
2
Entering edit mode
8.0 years ago
win ▴ 940

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 • 5.7k views
ADD COMMENT
2
Entering edit mode
8.0 years ago
Ying W ★ 4.2k

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

ADD COMMENT
1
Entering edit mode
ADD REPLY
0
Entering edit mode

thanks, just what i was looking for.

ADD REPLY
0
Entering edit mode
8.0 years ago
dwaggott ▴ 290

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

ADD COMMENT
4
Entering edit mode

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

ADD REPLY
0
Entering edit mode
13 days ago
Alireza ▴ 20

Also, The following script works well for this purpose.

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

ADD COMMENT

Login before adding your answer.

Traffic: 2061 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6