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Question about evaluation the HaplotypeCaller file

jackyhuangjackyhuang Taiwan,R.O.CMember
edited November 2019 in Ask the GATK team
Hi team,

I found two ways to evaluation the vcf file.
(1) VariantEval
(2) Concordance

The sequencing file I am using is NA12878, but I am not sure which vcf file to use.
If I use the b37_dbsnp_138.b37.excluding_sites_after_129file.vcf, the recall and precision is very bad.

Is it the evaluation vcf file is wrong?
Or is it because I didn't use b37_dbsnp_138.b37.excluding_sites_after_129file.vcf file for sequencing, so the result after verification is wrong?

Thank you,
Jacky

Answers

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