Using Music When Silent Mutation Is Excluded In Data

Question

[wangjiaqian]

Hello,

I have a problem when using Music. Only missense, nonsense, splicing mutations and indels are included in my data, there are no synonymous mutations, but the tumor do have synonymous mutations.

Is it OK to find SMGs with Music ? Is it OK to define background mutation without silent mutations?

Thank you~

Answer 1

[Cyriac Kandoth]

Read the arguments of music bmr calc-bmr, where it defaults to excluding Silent mutations. The documentation is online here. If you don't want MuSiC to skip Silent mutations, use the argument --noskip-silent.

But it is preferable to --skip-silent when finding SMGs with somatic mutations, because silent mutations are more likely to be passenger events with lower selective pressure during cancer evolution (though there are exceptions, like when Silent mutations alter promoter motifs). You can try running it with --skip-silent and --noskip-silent, and compare results.