Question: Variant distance bias (VDB) in VCF format: how to compute properly?
1
gravatar for Macspider
2.4 years ago by
Macspider3.1k
Vienna - BOKU
Macspider3.1k wrote:

Hi guys,

Does anyone of you have experience with computing the variant distance bias (VDB) value for VCF-formatted files?

I am trying to figure out myself how to do it, but literature / documentation / discussion on it is quite scarce.

So far, what I know is:

  • The higher the value, the bigger the bias is
  • 0 = no bias
  • It has to be a float

What is the range for such value? Does anyone have a ready-to-go formula to use? Are there any established rules of thumb that one can use to understand it?

I'm sorry if this question is trivial for someone, I'm a bit lost.

Thanks!

EDIT:

  • The range is [0,1] as a likelihood
bias distance variant vdb vcf • 610 views
ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by Macspider3.1k

See Vdb Field In Samtools for a discussion of this

ADD REPLYlink written 6 weeks ago by michael0
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