Forum:MutSigCV question: Why V1.3 and V1.4 have great different result?

Question

[bioxujintian]

Hello, everyone

I have 300+ cancer-normal matched samples, and use GATK+Mutect2+ANNOVAR to call somatic mutations and annotation, and R package maftools to transfer to MAF file. Then I use MutSigCV1.3 and MutSigCV1.4 to identify sinificance genes, but there is great different in number of genes with q-value<0.1,(13 and 138 respectively). So, I want to know how is the different came about?

Thanks all