How to merge the mutations from multiple samples of one patient

Question

[Rongxin]

Dear all,

Recently, I wished to use MutSig2CV_NC software link for the noncoding mutational analysis, which required me to provide a unique patient identifier. The fields required for the MutSig2CV_NC are listed below,

chr, pos, patient, ref_allele, newbase

However, I found that some specific patients may have multiple samples. The mutation data looks like this,

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• My question is how should I deal with these mutation data from different samples of the same patient.

• Are there any tools, pipelines, or tutorials to merge or deal with these mutation data?

Thank you for your time!

I am looking forward to your answers. Any questions, just feel free to comment.