samples off by one

[atimms]

Using the latest version of decon I'm getting a consistent error.
The first bam file is always described in the Failures.txt file as:
All Whole sample All Low correlation: 0.29554106282364, Low median read depth (FPKM): 0.405555555555556
In addition the CNV calls are always off by one so known CNVs are assigned to the incorrect sample.
Any help would be appreciated.
Andrew

[atimms]

this looks like an issue with the counts/ExomeCounts where the GC column is being assigned to the first sample and then all the samples are off by one.
Has anyone seen this or know of a resolution?

[fishcakess]

Has anyone seen this or know of a resolution?

Andrew change this part in the Rscript IdentifyFailures.R

colnames(ExomeCount)[1:length(sample.names)+4]=sample.names

Change that 4 to a 5 then save it.

[wcarre]

same issue in makeCNVcalls.R.
Ligne 69:
colnames(ExomeCount)[1:length(sample.names)+4]=sample.names
it should be
colnames(ExomeCount)[1:length(sample.names)+5]=sample.names

Otherwise all the samples / CNV are offsets.