gVCF files are incomplete

[muffato]

Description of the bug

gVCF files should contain 1 line for every position of the genome, however that's not the case for DeepVariant, cf google/deepvariant#484 . To check this, run the test mode, find a DeepVariant job, and compare the size of the gVCF to the size of the Fasta file.

We need a way of correcting the DeepVariant gVCF files, which may also fix the .het output (cf TOLSD-2540)

Command used and terminal output

No response

Relevant files

No response

System information

No response

[tkchafin]

https://github.com/google/deepvariant/blob/r1.8/docs/deepvariant-gvcf-support.md adding to look over later