Fix GT header in PostprocessGermlineCNVCalls's --output-genotyped-intervals output

[jmarshall]

PostprocessGermlineCNVCalls produces a GT header like this in one of its output files:

##FORMAT=<ID=GT,Number=1,Type=Integer,Description="Genotype">

which should have been Type=String. Incorrectly writing this as Type=Integer produces invalid VCF files and in particular causes bcftools to misparse records' genotype fields.

I searched for other similar problems and noted the inconsistencies in ReblockGVCFUnitTest.java. However this probably isn't causing any actual problems, so you may wish to include only the first commit — which very much is causing production problems.

[mwalker174]

Thank you @jmarshall the gCNV change LGTM. The first of many steps towards spec compliance in the GT field actually.

Would it be possible for us to merge after today's release to give users a chance to reconcile any downstream issues this introduces? I would imagine this could break some analysis scripts e.g. using pysam.

[jmarshall]

When to merge is your decision, but note that:

• Current production pipelines using bcftools are already broken by this
• Pysam currently misreads GT when given this header, so pysam-using analysis scripts are probably also already broken and/or contain workarounds. e.g. a basic for v in pysam.VariantFile(fname): print(v) loop produces the following (note the -65 instead of . for GT):

1	100	.	C	T	.	PASS	AN=4	GT:GQ	-65:245

[droazen]

@mwalker174 Since GATK 4.5 is now out, you can hit merge on this whenever you're comfortable.