Trouble when reproduce the

Question

Trouble when reproduce the

snower2010 opened this issue 5 years ago · 2 comments

snower2010 commented 5 years ago

Great Job!

I am running Clair on HG002 bam file and estimate its performance against Truth Variants by vcfeval in RTG tools. But the performance I got is really poor. The performance index are like around 10%. Even after I remove GA4GH low complexity regions from GIAB's high-confidence regions as described in Supplementary information, the index are still very low.
So could you please help to provide an script to reproduce you results or give me some advice?
Many thanks!

Answer 1 · 2020-05-26T05:46:40.000Z

You might want to take a look at the commands in the supplementary note of Clair's paper.

Answer 2 · 2020-05-26T06:51:15.000Z

Thanks for your quick answer! We refer to the supplementary note and code available on the github, but the results still seems un-satisfying. I will be very appreciate if there is not an end-to-end script to reproduce the process from variant calling to performance estimation.