Snp prediction accuracy is low in all difficult mapping areas

kishwarshafin / pepper

PEPPER-Margin-DeepVariant

MIT License

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Snp prediction accuracy is low in all difficult mapping areas #199

Open oranges7 opened 10 months ago

oranges7 commented 10 months ago

Hi, I use v3.1 stratification BED files,HG003 GUPPY3.6.0 data for testing, why the accuracy of snp and indel is not high，The results show that only 55%. I queried the results of Truth Challenge V2 and found that the accuracy of snp is more than 98%. What is the reason? The default parameters I use

oranges7 commented 10 months ago

Is this normal? I use bed files with high confidence regions, and the results are normal. Looking forward to your reply