About the coverage file

sibscc

Is the coverage_file necessary in Mutect analysis?
How to get the file?
Thanks.

Geraldine_VdAuwera

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.

Geraldine_VdAuwera

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.

sicotte

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.

In_Frame_Del DEL
In_Frame_Ins INS

Nonsense_Mutation TNP (early stop codon)
Nonstop_Mutation SNP (invalidated stop codon)

Splice_Site DNP
Splice_Site SNP

Translation_Start_Site DNP
Translation_Start_Site SNP

Sheila

@sicotte
Hi,

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.

-Sheila