search

dariober / cnv_facets

Somatic copy variant caller (CNV) for next generation sequencing
Other
67 stars 15 forks source link

LCN_EM=. ? #21

Closed wclee47 closed 4 years ago

wclee47 commented 4 years ago

Hi Dario, thanks for this program. In the output, some segments have LCN_EM set to ".". I think this might be different from the value "0". Do you have any idea how to interpret the value "." in LCN_EM?

Appreciated!

dariober commented 4 years ago

Hi - LCN_EM="." means the value is missing (NA). As to the reason why it happened and how to interpret it, I can't tell for sure especially without seeing the data. It may be the region is hypersegmented. Maybe the discussions at https://github.com/mskcc/facets/issues/62 and https://github.com/mskcc/facets/issues/50 help?

Keep in mind that cnv_facets is just a wrapper around the FACETS package so these sort of questions may be better answered by the developers of FACETS.

(Closing the issue now but feel to reopen)

Dario