Add additional input arguments to vc-gatk4-hc

[marcellevstek]

REID-2669

• Update CHANGELOG.rst for each commit separately:
  • Pay attention to write entries under the "Unreleased" section.
  • Mark all breaking changes as "BACKWARD INCOMPATIBLE:" and put them
    before non-breaking changes.
  • If a commit modifies a feature listed under "Unreleased" section,
    it might be sufficient to modify the existing CHANGELOG entry from previous
    commit(s).
• Bump the process version:
  • MAJOR version (first number): Backward incompatible changes (changes
    that break the api/interface). Examples: renaming the input/output, adding
    mandatory input, removing input/output...
  • MINOR version (middle number): add functionality or changes in a
    backwards-compatible manner. Examples: add output field, add non-mandatory
    input parameter, use a different tool that produces same results...
  • PATCH version (last number): changes/bug fixes that do not affect
    the api/interface. Examples: typo fix, change/add warning messages...
• All inputs are used in process.
• All output fields have a value assigned to them.

[marcellevstek]

@jkokosar I did not check the output BAM in IGV, as I assume the tools outputs it correctly.

Here is the documentation for the version we are using:
https://gatk.broadinstitute.org/hc/en-us/articles/4414586765723-HaplotypeCaller

[jkokosar]

Please check if the output BAM file is position sorted. Add index file to the separate output field.

[jkokosar]

LGTM