I am trying to identify copy number variation in tumor/normal data using the workflow on the VarScan page. I got as far as the last step, where I got stuck on input to mergeSegments.pl mergeSegments.pl says that it requires the following fields in the input:
USAGE: mergeSegments.pl [segments] OPTIONS segments - A segments file with p-values from the DNAcopy library. This should be tab- or space-delimited with a header and the following columns: ID, chrom, loc.start, loc.end, num.mark, seg.mean, bstat, pval, lcl, ucl.
Meanwhile, the R script given on the workflow page produces a file with only the following fields:
ID chrom loc.start loc.end num.mark seg.mean
(even if I write out all columns of segs$output, where segs is the result of calling the segment function in DNAcopy)
My question is: where and how do I get the remaining coumns (bstat, pval, lcl, ucl) for input to mergeSegments.pl?