Calculating probability of a false positive variant
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21 months ago
drabiza1 ▴ 20

Ive sequenced 500 samples and performed variant calling. 3 of those samples are from the same individual. All the samples have a certain number of false positives. Some of the false positives are recurring and some are only seen once in the dataset. I found a certain variant that is called in the 3 samples from the same individual but in none of the 497 samples, but each of the 3 times it was identified, the variant was flagged as a false positive.

Is there some statistical method people use to identify the probability that this a false positive in this context?

VCF GATK Variant Calling • 345 views

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