Question: regions with very different VAF fall into one cluster
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gravatar for sm.hashemin
8 months ago by
sm.hashemin80
sm.hashemin80 wrote:

Hi Chris, I was wondering, how come some variation with very different VAF fall into one cluster? [clusters] https://ibb.co/kbHThf

sciclone • 254 views
ADD COMMENTlink modified 6 months ago by Chris Miller21k • written 8 months ago by sm.hashemin80
1

It made me wondering!

ADD REPLYlink written 6 months ago by sm.hashemin80
1

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.

ADD REPLYlink modified 6 months ago • written 6 months ago by genomax69k
1

Thanks a lot, you are a life saver.

ADD REPLYlink modified 5 months ago • written 5 months ago by sm.hashemin80
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gravatar for Chris Miller
6 months ago by
Chris Miller21k
Washington University in St. Louis, MO
Chris Miller21k wrote:

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?

ADD COMMENTlink written 6 months ago by Chris Miller21k
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