Question: Gold standard variant set
0
gravatar for rse
14 months ago by
rse90
Singapore
rse90 wrote:

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

sequencing next-gen genome • 529 views
ADD COMMENTlink modified 14 months ago • written 14 months ago by rse90
1

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.

ADD REPLYlink written 14 months ago by WouterDeCoster42k

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

ADD REPLYlink written 14 months ago by rse90

You cannot create a ground truth set without an orthogonal technique.

ADD REPLYlink written 14 months ago by WouterDeCoster42k

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.

ADD REPLYlink written 14 months ago by Devon Ryan93k
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