Genotype quality

[MikeWLloyd]

Can you clarify the following: indel_header.addFormatField("GQ", "1","String", "Genotype quality (currently not supported. Always 0)");

There are non-zero GQ values in the final VCFs. I am confused by the header statement.

[cmnbroad]

Also, the 4.x versions of the vcf spec all state that GQ is an integer. Having said that, according to github, the particular line referenced above is 8 years old, and its entirely possible that the early 4.x specs incorrectly stated GQ was string (and there is STILL an incorrect example in the 4.3 spec that uses String as well).

[MikeWLloyd]

For what it is worth, 'PL' is also out of spec.

##FORMAT=<ID=PL,Number=.,Type=Float,Description="Normalized likelihood of the current genotype">

I believe this should be 'Integer' as well.