Question: regions with very different VAF fall into one cluster
0
gravatar for sm.hashemin
3 months ago by
sm.hashemin60
sm.hashemin60 wrote:

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

sciclone • 127 views
ADD COMMENTlink modified 5 weeks ago by Chris Miller20k • written 3 months ago by sm.hashemin60
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 weeks ago • written 6 weeks ago by genomax62k

Thanks a lot, you are a life saver.

ADD REPLYlink modified 20 days ago • written 20 days ago by sm.hashemin60

It made me wondering!

ADD REPLYlink written 6 weeks ago by sm.hashemin60
1
gravatar for Chris Miller
5 weeks ago by
Chris Miller20k
Washington University in St. Louis, MO
Chris Miller20k 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 5 weeks ago by Chris Miller20k
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