silent and nonsilent rates are too different  We run the
analysis using Mutect and annovar,after that we input the
annotated data into MutSig. However, it gave the error message:
silent and nonsilent rates are too different  Any clue why
MutSig spit out this error?   We have also got the same  We have
also got the same error, going through the code it seems ratio
of # nonsilent rate/ # silent rate (#nonsilent rate = # non
silent/sum of coverage of all nonsilent mutations) should be
between 0.5 to 2. The error that we are getting could be due to
fact we are using full exome coverage file, trying to create a
coverage file our own sample.  Why are silent and non-silent
rates too different?  In general, MutSig estimates the
background mutation rate by looking at the silent to non-silent
mutation rates, which in turn is used to calibrate the p and q
values, and to correct for per-gene differences in background
mutation rate.  In some cases, all the silent mutations get
filtered out of the maf file before the user