regions with very different VAF fall into one cluster
1
0
Entering edit mode
2.7 years ago
sm.hashemin ▴ 90

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

sciclone • 639 views
ADD COMMENT
1
Entering edit mode

It made me wondering!

ADD REPLY
1
Entering edit mode

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 REPLY
1
Entering edit mode

Thanks a lot, you are a life saver.

ADD REPLY
1
Entering edit mode
2.5 years ago

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 COMMENT

Login before adding your answer.

Traffic: 2752 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6