0 rows in vcf.data.filtered VCF object

[gsatas]

Hi, I'm attempting to run FIREVAT on Mutect2 (GATK4) output, and running into the problem that all variants are removed after initialization. This is the end of the output I'm receiving:

...
[1] "INFO [2023-06-14 15:19:40] * Checking if given mutations are point mutations."
[1] "INFO [2023-06-14 15:19:40] * Removing VCF rows with NA parameters."
[1] "INFO [2023-06-14 15:19:41] * After initialization:"
[1] "INFO [2023-06-14 15:19:41] ** 0 rows in vcf.data.filtered VCF object."
[1] "INFO [2023-06-14 15:19:41] ** 616254 rows in vcf.data.artifact VCF object."
[1] "INFO [2023-06-14 15:19:49] Step 01-5. Make VCF filter [firevat_filter::MakeFilter]"
[1] "INFO [2023-06-14 15:19:49] Step 01-6. Prepare data for optimization"
[1] "INFO [2023-06-14 15:19:49] Step 01-7. Check mutations count"
[1] "WARNING [2023-06-14 15:19:49] FIREVAT must have at least 50 mutations to run. Returning without running FIREVAT."

I'm starting with the provided Mutect2 configuration file, and the only change I make to it is renaming "NORMAL" to the name of the normal sample in my experiment. I am then running firevat with this command (adapted from the example in the README):

results <- RunFIREVAT(vcf.file = sample.vcf.file,
                      vcf.file.genome = 'hg19', # for mouse variants: 'mm10'
                      config.file = mutect2.config.file,
                      df.ref.mut.sigs = GetPCAWGMutSigs(),
                      target.mut.sigs = GetPCAWGMutSigsNames(),
                      sequencing.artifact.mut.sigs = PCAWG.All.Sequencing.Artifact.Signatures,
                      output.dir = output.dir,
                      objective.fn = Default.Obj.Fn,
                      num.cores = 2,
                      ga.pop.size = 100,
                      ga.max.iter = 5,
                      ga.run = 5,
                      perform.strand.bias.analysis = TRUE,
                      ref.forward.strand.var = "TumorDPRefForward",
                      ref.reverse.strand.var = "TumorDPRefReverse",
                      alt.forward.strand.var = "TumorDPAltForward",
                      alt.reverse.strand.var = "TumorDPAltReverse",
                      annotate = FALSE)

Is there any way to identify what the filter is that is removing all variants? Thank you for any help!

[khb7840]

As default, NORMAL is at column 10 and TUMOR is at column 11. With Mutect2 config file, FIREVAT reads AD, AF, F1R2, F2R1 in FORMAT and TLOD, NLOD, MBQ, MMQ in INFO. Please check if these variables exist in your vcf file.