Hi all,
I had a look at the wiki and I see there are many tools available for getting copy number changes from read alignments. I am wondering if there is a particular accepted tool that comes most highly recommended.
I am most often comparing 30X tumour to 30X normal, and I know from experience that GC bias correction is necessary.
Freec seems like a good candidate however, when comparing matched tumour normal pairs the applied bias correction seems a little less vigorous than I would like.
Any information is appreciated!
I had a look at the wiki and I see there are many tools available for getting copy number changes from read alignments. I am wondering if there is a particular accepted tool that comes most highly recommended.
I am most often comparing 30X tumour to 30X normal, and I know from experience that GC bias correction is necessary.
Freec seems like a good candidate however, when comparing matched tumour normal pairs the applied bias correction seems a little less vigorous than I would like.
Any information is appreciated!
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