Is the coverage_file necessary in Mutect analysis?
How to get the file?
It is not necessary but you can get MuTect to generate it using the --coverage_file argument.
For a list of all arguments to MuTect, run
java -jar target/mutect-1.1.7.jar -T MuTect --help
from the command line. You may need to adapt the name and file path of the mutect.jar file.
What if we did not use Mutect and have to create our own?
Are the following mutations to be considered "null"? or just like missense.
Nonsense_Mutation TNP (early stop codon)
Nonstop_Mutation SNP (invalidated stop codon)
What exactly are you trying to do? If you are using MuTect2 in GATK3 or Mutect2 in GATK4 (recommended), you do not need a coverage file.