Fix potential bug in VCF Integration test

[gbggrant]

Doesn't appear to be comparing the VCFs, only the headers.

[gbggrant]

Passing job here
Look at the logs for AssertIdenticalOutputs and you'll see that it's actually comparing the VCFs in this PR.
Previously passing run here

[mcovarr]

oh that does look like a bug 😬

[codecov]

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Additional details and impacted files

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