VariantEval - explanation of output fields?
Posted in Ask the team | Last updated on 2013-01-09 03:06:09


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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


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