I am interested in assessing the clonality of a tumor sample I have which is also paired with a normal tissue control from the same patient (~30x coverage). Specifically, I would like to know if there are any significant sub-clones present within the tumor sample.

I have come across numerous tools which look like they may be able to help me, including: [cloneHD][1], [SubcloneSeeker][2], [ABSOLUTE][3], [CITUP][4], [THetA2][5], [PhyloWGS][6] .. others?

Does anybody have an experience using any of these tools, or any thoughts on which one I should try out?

 [1]: http://www.sciencedirect.com/science/article/pii/S2211124714003738
 [2]: http://www.genomebiology.com/2014/15/8/443
 [3]: http://www.nature.com/nbt/journal/v30/n5/full/nbt.2203.html
 [4]: http://bioinformatics.oxfordjournals.org/content/31/9/1349.full
 [5]: http://bioinformatics.oxfordjournals.org/content/30/24/3532.full#ref-6
 [6]: http://www.genomebiology.com/2015/16/1/35
We've been working on integrating clonality and heterogeneity estimation tools into bcbio (https://github.com/chapmanb/bcbio-nextgen). It's still a work in progress but we've been evaluating against internal datasets where we have external predictions of normal contamination. We've had the most success with:

 - Battenberg from Sanger (https://github.com/cancerit/cgpBattenberg). This calls CNVs and provides estimates of normal contamination. It's also a required input for PhyloWGS.
 - PhyloWGS. We don't currently have a way to validate heterogeneity but get a useful set of trees to estimate how much of a mix is in a tumor sample.
 - BubbleTree from MedImmune (http://www.bioconductor.org/packages/release/bioc/html/BubbleTree.html) which provides estimates of normal contamination and also clonality. We haven't dug much into the heterogeneity estimates of this yet.

We also looked at THetA2, but didn't have good luck with it, so spent more time with the above three tools.

Hope this helps provide some useful directions.