I am working on eliminating false positives while disease gene hunting. Often across searches (and across diseases) I find the same genes popping up as top candidates. We have multiple lines of evidence that these are false positives from biological and in silico data.
A neat paper highlights several of the genes that are common false positives.
Taxonomizing, sizing, and overcoming the incidentalome
I am looking for (healthy or sick) TruSeq Exome Enrichment Kit exomes. I plan on running the raw data through my pipeline and mixing them into my larger background.
Does anyone know where I can get raw reads from TruSeq Exome Enrichment Kits or variant calls?
Would anyone be willing to share these data for use a control?
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Zev.Kronenberg
You might take a look at the Exome Sequencing Project site. You can download VCF files from variant calls representing thousands of samples.
The dataset at this site makes a big difference. >5400 exomes at present, and growing. If your variant of interest is present here, it's probably not disease causing. If it's absent from this dataset, then you've got a rare variant, and can probably justify moving forward with validation.
Nice resource. I have browsed their SNVs, but never downloaded it. Downloading now.
Do you know if there is a way to get individuals genotypes rather than allele frequencies?
I don't believe there is a way to get individual genotypes; I imagine this is due to privacy concerns.
Have you checked ENA ?
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Are you looking for fastq files or VCFs ?
I will take either, but I really want them to be from the same capture array.