I was wondering, how come some variation with very different VAF fall into one cluster?
It made me wondering!
Are you addressing this question to a specific user on biostars? You can't just say Hi Chris and expect that specific person to respond. You could look up their user profile link (e.g. this is your own https:// www.biostars.org/u/46755/ , space added after // to prevent biostars code from parsing the link) and then tag the user (e.g. sm.hashemin ) here.
Thanks a lot, you are a life saver.
You have not removed copy number altered variants from.your sample (this includes variants on sex Chris in males). Anything at 100% vaf is almost certainly in a CN1 region and needs to be excluded.
See this post (and several others under the "sciclone" tag) for additional context sciClone package -> mosaic copy number correction of VAFs?
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