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.
•
written
by
miller.3.katie •
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
Thanks Raony! Are the miller and schinzel_giedion vcf files aligned to hg18 or hg19?
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.
That's actually great advice!
Log in to answer this question.
