QCTOOL should write PHRED-scaled probabilities in VCF

Issue #9 closed
Gavin Band
repo owner created an issue

Currently QCTOOL outputs 'GP' field in VCF files but the contents are unscaled probabilities. However, the VCF format specified these should be PHRED-scaled probabilities. Here is one way of going about it suggested by Warren Kretzschmar:

  • switch to using phred scaled probabilities in the next release
  • use a command line switch for legacy support of unscaled genotype probabilities for input and output
  • test all input genotype probabilities to see if they look like they are unscaled and die with the requirement for a "force phred scaled input genotype probabilities" command line switch if the input looks too much like unscaled genotype probabilities.

Some tests that might be useful: - do the probabilities sum very close to 1? - are any of the probabilities substantially greater than 1?

Also, I think the GP field is not documented in the qctool documentation. It would be good to document how the GP field is interpreted in any case.

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