Hi all,
I have a question about GIAB confidence region! I know it is normally used for benchmarking. But when people do variant calling from their sample. Is it ok to say that variant called from the confidence region is real?
Thanks!
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written
by
Jian •
1 answer
Those are very specific to individual samples in GIAB. There are literally different confidence region files for HG002, HG003, and HG004 for instance.
The high-confidence regions are really geared toward defining the areas that were fair game for the benchmarking studies. They aren't supposed to be used for evaluating individual variant calls.
You'll know if you have low coverage (DP). You'll know if you have trouble mapping (MAPQ). These are all considered when computing the genotype quality (GQ).
Use your genotype quality score when talking about called variants for sample A.
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