What capture kit are you using? Matching that, if possible, makes the resulting data a lot cleaner
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I am going to pick the kit based on the normals.
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Why one would want to make a database of somatic cnvs? Recurrent genes affected by cnvs by cancer type are better described in corresponding publications.
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I don't want to make a database of somatic CNVs. I need a database of normals to serve as the control for CNV calling in new samples so we don't pick up, e.g. artifacts of the exome kit.
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1kg is still the largest set of unrestricted exomes available (AFAIK). I’m sure you already know the raw data for UKB and GnomAD are not (easily) available (also TOPmed).
@konradjk might have a list of additional exomes (beyond 1kg) they use in GnomAD that are unrestricted. -
Presuming the methods are too far diverged to use gnomad site information? If so then 1KG + HGDP would be my quick suggestion, both now with high coverage genomes
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This is awesome, thank you for the resource! I didn't know this existed.
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@ryanlayer might also be a good resource. -
I hate to be a hater, but this may be a lost cause. The 1kg exomes are so old that I don’t think they will be much help, also a ton of variability within those exomes since they were done at different sites. If you have ~30 of your in-house exomes I would just stick with those
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