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starskyzheng / panpop

Application of pan-genome for population
MIT License
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使用PART模块后如何计算准确率和召回率？ #51

Closed zhengluo-lz closed 2 months ago

zhengluo-lz commented 3 months ago

郑博士您好！ 当我们使用其他SV分型的软件对二代reads的群体进行SV分型后，再使用PART模块进行SV的合并，请问有好方法对合并后的准确率和召回率进行评估吗？

starskyzheng commented 3 months ago

您可以看我的NC文章，里面有写方法

zhengluo-lz commented 3 months ago

您可以看我的NC文章，里面有写方法

我看文章里用的方法是Truvari的bench方法，使用的参数是 -p 50 -P 50 -r 500，但我看这个软件的参数说明Min sequence similarity. Set to 0 to ignore (0.7)和Min variant size similarity (0.7)的阈值范围应该是0-1吧，这个是文章里面写错了吗

starskyzheng commented 3 months ago

不好意思，确实写错了，是0.5 --pctsim 0.5 --pctsize 0.5 --refdist 500

github-actions[bot] commented 2 months ago

This issue is stale because it has been open for 30 days with no activity.

github-actions[bot] commented 2 months ago

This issue was closed because it has been inactive for 14 days since being marked as stale.