Publicly-available disease genome VCF

Question

[miller.3.katie]

Does anyone know if/where I can download publicly-available VCF (sequence variant file) from a rare disease subject, preferably with the causal variant known? We want to test an app we developed that inputs VCF files. We would potentially put this VCF on a public server, so we need a file that is freely accessible to the public, not a file that we need to gain access or permissions to.

Answer 1

[Raony Guimarães]

Here you can find a few examples:

https://github.com/raonyguimaraes/mendelmd/tree/master/examples

NA12878.compound_heterozygous.vcf.gz
NA12878.dominant.vcf.gz
NA12878.recessive.vcf.gz
NA12878.xlinked.vcf.gz
miller.vcf.gz
schinzel_giedion.vcf.gz

[miller.3.katie]

Thanks Raony! Are the miller and schinzel_giedion vcf files aligned to hg18 or hg19?

Answer 2

[Samuel Brady]

The Yandell lab has normal genomes spiked-in with disease variants (real disease variants but not possessed by those individuals) that comes with their VAAST software (see bottom of page 5):

http://www.yandell-lab.org/software/VAAST/VAAST_Quick-Start-Guide.pdf

However, it is in GVF instead of VCF format, but you can convert as described here: Convert GVF to VCF.

You might consider doing the same thing though - find normal publically available exomes and spike in known disease variants.

[WouterDeCoster]

That's actually great advice!