Update variationReference.avdl

We've clarified some language and asked some questions where we are unsure.
No, you are not required to provide probabilities.  Which fields are used typically depend on what stage in the pipeline has been reached, what the
depth of sequencing is, and what the purpose of the data set is.   

Yes, the likelihood field corresponds to the genotype likelihood (GL) field in VCF, though they are Phred scaled (-10 log_10()).  So likelihoods 0.1, 0.01, 0.001 convert to 10, 20, 30 respectively.  Should we also require Phred scaling in the avro?
The probability field corresponds to the GP field.  Again, we should be clear whether this in in phred units.
My preference is to keep phred scaling for continuity.  Phred is easier to look at when trying to understand what is going on, and can be 
truncated to the nearest integer without damaging accuracy much.  But in the avro interface we do have the chance to switch if we want.

Richard

On 7 Jul 2014, at 18:56, Frank Austin Nothaft <notifications@github.com> wrote:

> In src/main/resources/avro/variationReference.avdl:
> 
> >  
> >    // not all of the following will be present, but at least one should be
> > -  int copyNumber ;	     // 0 for not present, 
> > -  float dosage ;
> > -  array<float> probability ; // probability copy number is k: 0..n
> > -  array<float> likelihood ;  // likelihood of data given copy number k
> > -  int readCount ;	     // number of reads supporting this allele (DP in VCF)
> > -  array<GAKeyValue> evidence ; // potential other evidence for the call
> > +  union { null, int } copyNumber = null ; // 0 for not present in callSet, 1 for single copy, 2 for 2 copies etc. 
> > +  union { null, float } dosage = null ; // expected value of copyNumber
> > +  array<float> probability = [] ; // probability that copy number is k: 0..n
> The documentation of this field is a little ambiguous. If I provide data for this field, am I required to provide a probability for all copy number values on [0, n]? Ditto for the likelihood field. I take it that the likelihood field is equivalent to the genotype likelihoods field in VCF?
> 
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