[VCFtools-spec] VCF Pedigrees: Determining/specifying the sex of children

[Len T. <len...@re...>]

Currently the VCF spec allows pedigree information to be encoded, in
the form:

##PEDIGREE=<Name_0=G0-ID,Name_1=G1-ID,...,Name_N=GN-ID>

And further in the spec it gives an example for a family relationship as:

##PEDIGREE=<Child=CHILD-GENOME-ID,Mother=MOTHER-GENOME-ID,Father=FATHER-GENOME-ID>

From this example it is possible to infer the sex of the parents but
not the children. What is the recommended way of indicating the sex of
the children in the pedigree? Should the recommended pedigrees instead
be to use one of:

##PEDIGREE=<Daughter=CHILD-GENOME-ID,Mother=MOTHER-GENOME-ID,Father=FATHER-GENOME-ID>
##PEDIGREE=<Son=CHILD-GENOME-ID,Mother=MOTHER-GENOME-ID,Father=FATHER-GENOME-ID>


Alternatively, should there be the concept of a genome header declaration?

##GENOME=<ID=GENOME-ID,Sex=SEX>

e.g.:

##GENOME=<ID=FATHER-GENOME-ID,Sex=Male>
##GENOME=<ID=MOTHER-GENOME-ID,Sex=Female>
##GENOME=<ID=CHILD-GENOME-ID,Sex=Male>
##GENOME=<ID=CHILD-GENOME-ID2,Sex=Female>

(I personally think using Daughter/Son in the PEDIGREE line is the
simplest solution.)

Cheers,
Len.