Describe the issue

When using maftools to plot mutational summary data, I encountered some issues:

1. I use WES data to generate a filtered VCF file, and then utilize VEP for annotation to obtain an MAF file.
2. The MAF file contains an excessive number of missense mutations, with up to 10 missense variants occurring in a single gene.
3. Furthermore, the plot generated by maftools displays an overwhelming amount of multi_hit annotations.
4. All genes exhibit a 100% occurrence rate.
5. I'm uncertain as to which step may have led to this issue.

If there is any additional information I should provide to resolve this issue, please do not hesitate to let me know.

Thank you very much.

Command

library(maftools)

laml <- read.maf('vep_merge.maf')

plotmafSummary(maf = laml, rmOutlier = TRUE, addStat = 'median', dashboard = TRUE, titvRaw = FALSE)

oncoplot(maf = laml, top = 30,showTumorSampleBarcodes = F)