Filtering out mutations from cancer dataset

Question

[Pappu]

I want to filter a list of thousands of possible mutations from a cancer NGS dataset. I am wondering which tool is suitable for this purpose. Is there any way to identify mutations which alter protein folding, structures or interactions with other proteins or DNA or RNA?

[andrew.j.skelton73]

Is this for use with RNA or DNA Sequencing? Why are you trying to filter out mutations? What kind of mutations do you want to remove? - Your question is vague, you need for detail and context to what you're trying to achieve

[ivivek_ngs]

Please detail you question regarding the nature of mutation you are intending to interrogate, there can be multiple ways to grep mutations you are interested in. Clarify if you have WGS, WES or RNA-Seq data and then you must specify if it is having vcf file or annotated file post vcf formation. In any case you will have the functional annotation of the mutations once they are annotated using any of the tools like annovar, VEP or snpEFF. Then you can do following non-synonymous and synonymous filtering and then look deeper at feature categories which states the various non-synonymous features.