I'm having a try with sciClone for my exome-seq data. It work fine in the one-sample running but an error reported when using two samples (tumors from two different individuals) for comparison.
I use the SNV and CNA information.
The SNV file format:
contig position t_ref_count t_alt_count tumor_f (all tab-delimited)
The CNA file format: chr, start, stop, segment_mean (which is followed by the VarScan and DNAcopy processing pipeline)
The code used in the two sample comparison:
sc = sciClone(vafs=list(v1,v2),copyNumberCalls=list(cn1,cn2), sampleNames=names[1:2],cnCallsAreLog2=TRUE,minimumDepth=50)
But only reporting this error:
 "checking input data..."  "Not all variants fall within a provided copy number region. The copy number of these variants is assumed to be 2."  "Not all variants fall within a provided copy number region. The copy number of these variants is assumed to be 2."  "ERROR: no sites are copy number neutral and have adequate depth in all samples"
I've tried changing the minimumDepth value but still can't work. The SNV and CNA file header names shouldn't be the problem since I deleted the header (reading file with: read.table(file)) the problem still exist.
Appreciating anyone's help.