CNV calling on tumor sample with no germline counterpart

Question

[Bogdan]

Dear all,

please would you recommend the algorithms/software that perform CNV calling on WGS data of TUMOR sample with NO GERMLINE counterpart ? Many thanks,

-- bogdan

[guillaume.rbt]

I personally use Delly2, which seems to work well (I'm working on haploid fungi)

[linouhao]

hi,have you tried canvas? thanks a lot.

Answer 1

[Eric T.]

Canvas and CNVkit can do it.

[Bogdan]

thank you Eric, it is very informative ;)