Refining tumor/normal assignment

[nandobonf]

Dear authors,
I successfully ran Numbat on multiple samples, however in some cases I would need to refine the tumor/normal definition (or eventually remove "noisy" CNV calls such as the BAMP). In the case shown below, for example, it is clear that genotypes 1 and 2 demote normal cells, instead, Numbat only calls genotype 1 as "normal". You can see the Numbat tumor/normal annotation labeled as "type" in the heatmap below.
Any suggestions would be highly appreciated.
Thanks in advance.

[teng-gao]

Hi,

In this case you can add up probabilities of clone_1 and clone_2 (fromclone_post) and use that as normal probability. This works because clone_post contains clonal assignment probabilities, and for each cell they sum to one.

Best,
Teng