Bug Bulletin: we have identified a bug that affects indexing when producing gzipped VCFs. This will be fixed in the upcoming 3.2 release; in the meantime you need to reindex gzipped VCFs using Tabix.

VariantEval - explanation of output fields?

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

VariantSummary:

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

TiTvVariantEvaluator:

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

CountVariants:

  • 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,

Jeremy

Post edited by Geraldine_VdAuwera on
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