How is better perform the analyze the somatic mutations? (the mutations of my interest gene)
Entering edit mode
16 months ago
Sonia • 0

Hi all,

I have 14 interest proteins and want to know how does their genetic status change during cancer (which somatic mutations occur in their genes?). To this aim, I started analysis on the VCF files of 80 patients. I proceeded according to the following steps:

  1. Annotation of VCF files
  2. Using a bed file to separate my interest genes among all variants
  3. Filtering the mutations that occur in exonic loci
  4. ?
  5. ?

And now I do not know how to continue my analysis? Can I visualize them with an Oncoplot?

Thank you for letting me know if you have any suggestions for further analysis or point me to related articles.

somatic VCF annotation Oncoplot • 373 views
Entering edit mode

you certainly can visualize them with oncoplot.

I don't understand what is genetic status in "how does their genetic status change during cancer".

in order to tell which somatic mutations occur you need normal and cancer tissues sequenced and normal mutations substracted from cancer ones.


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