Multiple tumors should be able to share the same matched normal - Githubissues

IARCbioinfo / needlestack

Multi-sample somatic variant caller

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Multiple tumors should be able to share the same matched normal #153

Closed mfoll closed 4 years ago

mfoll commented 7 years ago

This is a common experiment design:

biological replicates
technical replicates
multiple regions of a tumor sequenced
temporal sequencing of the same tumor etc. Currently it is crashing in needlestack.r because these lines return vectors instead of a single numerical value:
```
Tindex = sapply( 1:nrow(TNpairs.complete) , function(k) return(which(indiv_run[,2]==TNpairs.complete$TUMOR[k])) )
Nindex = sapply( 1:nrow(TNpairs.complete) , function(k) return(which(indiv_run[,2]==TNpairs.complete$NORMAL[k])) )
```
The problem is that it interferes with the GERMLINE status as a normal will have multiple tumor. I propose in this case to simply take the first one to assign the status. Similarly, if someone decide to put multiple normal for the same tumor we can simply take the first one. In practice I think only adding [1] after the two which(...) above would do the trick.

mfoll commented 7 years ago

@nalcala what do you think? do you see something I am missing?

tdelhomme commented 6 years ago

@nalcala Was this fixed?

tdelhomme commented 6 years ago

don't think, maybe we can shifted to next version.

mfoll commented 6 years ago

I think I remember this was actually already possible and no change was needed