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5.6 years ago
rse
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100
Hi, I want to compare different variant calling pipelines for an exome sample. But, I don't know what gold standard to use for evaluation of performance parameters (sensitivity, specificity, etc). Can anyone suggest me how to create a gold standard for my exome. The genome in a bottle contain gold standard variants for the individual "NA12878" and I presume I cannot use that. Thank you in advance
Regards
Meaning you have sequenced a specific sample and want to compare pipelines?
By the way, while this might be interesting for you, this has been done hundreds of times. For a recent good comparison see this paper.
Yes, i have sequenced my sample and want to compare pipelines. Thank you for suggesting this reference paper. Is there any more studies describing the process of generating a gold standard dataset for our sample? Thanks
You cannot create a ground truth set without an orthogonal technique.
Why do you want to create your own gold standard? The thing about gold standards is that you only make one of them, since they're a lot of work.