Jointsnvmix ran on rnaseq data

[Xiangqian Guo]

Hi,

Can you use jsm.py on rnaseq data to call the mutation?

Thanks.

X.

[aroth]

Hi Xiangqian,

Apologies for the long delay. Theoretically JointSNVMix could be used on RNASeq data if you had tumour normal pairs. This would only be beneficial if your current strategy for calling somatic mutations had a high number of germline false positives. There are some issues with RNASeq such as highly uneven coverage which may also lead to problems for JointSNVMix. In addition JointSNVMix can be confused by technical artifacts since it doesn't perform any heuristic filtering post-hoc like many other tools.

Cheers,

Andy