maftools do not find differentially mutated genes while bcftools isec have a lot of locus for each compared sample

Question

[omicsresearch]

Dear guys,

When trying to use maftools to compare mafCompare() to compare the whole exome data maf file (only keep the mutations with PASS), it shows "No deferentially mutated genes found",

while when using the bcftools isec to compare the two vcf files(say A.vcf.gz B.vcf.gz), there do have a lot of mutations private to A or B.

When using the vcf-compare vcf-compare -p plot A.vcf.gz B.vcf.gz, do not output the plots.

Thank you very much for all your guidance!