The current GATK version is 3.7-0
Examples: Monday, today, last week, Mar 26, 3/26/04

Howdy, Stranger!

It looks like you're new here. If you want to get involved, click one of these buttons!

Powered by Vanilla. Made with Bootstrap.
GATK 3.7 is here! Be sure to read the Version Highlights and optionally the full Release Notes.
Register now for the upcoming GATK Best Practices workshop, Feb 20-22 in Leuven, Belgium. Open to all comers! More info and signup at

VariantEval - explanation of output fields?

Jeremy37Jeremy37 Member Posts: 5
edited January 2013 in Ask the GATK team

Hello, I've just started using VariantEval. It seems very useful and provides a good deal of output.
However, it's not obvious to me what all of the fields mean. Do you know when there will be documentation of the output?

For example, some things I'd like to know:


  • What is the difference between TiTvRatio and TiTvRatioPerSample?
  • What is SNPNoveltyRate? (In general I don't understand the rate fields)


  • What is TiTvRatioStandard? What are the nTiDerived and nTvDerived fields?


  • What are variantRate and variantRatePerBp? Is variantRatePerBp the average number of bp between variants? (If anything it seems like the names for these should be reversed.)
  • What are heterozygosity and heterozygosityPerBp?

What is the --dbsnp parameter used for? Is this redundant with --comp?

Many thanks for your help,


Post edited by Geraldine_VdAuwera on


Sign In or Register to comment.