Hi,

I found two ways to evaluation the vcf file from gatk. (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