Hello,

after a check of the number of raws in maf files and amount of variants reported by maftools in sample summary I see very different numbers:

maf (grep -v "#"|wc)     maftools (sampleSummary - total)
sample A: grep: 929 maftools: 281

sample B: grep: 5480 maftools: 1598

Have you got any idea about what can be a reason?

Thank you very much,
Martina