Venter Genome Vcf

Question

[win]

Hi all, I was wondering if there was a VCF version of Venter's genome? There is a GFF file but not sure if there was a VCF file?

Thanks in advance.

[ericrkofman]

I can't find an hg38 version, and the old VCF seems to be of a different header format so I am having difficulty converting it to hg38 from hg19. Anybody have an hg38 update for this?

Answer 1

[Emily]

We've got it on the Ensembl FTP site.

[win]

thanks, just what I was looking for.

[Dan D]

Please be sure to mark her answer as accepted.

[Endre Bakken Stovner]

Wonderful! Even updated to latest genome version.

Do you have a full genome version of Venter/Watson updated to hg38 somewhere?

[Emily]

We just have the VCF.

[Tawny]

The link above appears to be broken. Does anyone have the new link?

[jpuntomarcos]

This other link is currently working.

[Jeremy Leipzig]

there are some violations in this VCF:

• Invalid count number, with fixed count the number should be 1 or higher: key=INFO name=TSA type=String desc=Type of sequence alteration
• Key GT found in VariantContext field FORMAT at chr1:13001418 but this key isn't defined in the VCFHeader

Answer 2

[Dan D]

Here's a SNP list. It's not VCF, but it contains similar data.