Mutect2 vcfs improperly formatted

[drejom]

Describe the bug
A clear and concise description of what the bug is.
Mutect2 vcfs missing DP in the FORMAT column (present only in INFO column). This is fixed in gatk version >4.0.9.0 (Sarek release 2.1.1 uses gatk 4.0.6.0)

To Reproduce
Steps to reproduce the behavior:

1. Command line '...'
   somaticVC.nf --tools mutect2

2. See error Please provide your error message
   No error is reported

Expected behavior
A clear and concise description of what you expected to happen.
DP should be reported in the FORMAT field. Makes VCFs produced by Sarek 2.1.0 incompatible with some R packages, eg VariantAnnotion and seqCAT

System (please complete the following information):

• Hardware: [e.g. HPC, Desktop, Cloud...]
• Executor: [e.g. slurm, local, awsbatch...]
• OS: [e.g. CentOS Linux, macOS, Linux Mint...]
• Version [e.g. 7, 10.13.6, 18.3...]

Nextflow (please complete the following information):

• Version: [e.g. 0.31.0]

Container engine (please complete the following information):

• Engine: [e.g. Conda, Docker or Singularity]
• version: [e.g. 1.0.0]
  Singularity

Container (please complete the following information):

• tag: [e.g. 1.0.0]
  2.1.1
  Sarek (please complete the following information):
• version: [e.g. 2.1.0]
  2.1.1

Additional context
Add any other context about the problem here.