I am a little new to this so any help would be appreciated - I ran a variation of the standard example workflow for VarScan2 copy number variant caller (using my exome sequencing data). I visualized the results of the segmentation (Step 4 - first few lines of output shown below) and it looks good, so I am now trying to implement Step 5: Merge adjacent segments of similar copy number and classify events by size (large-scale or focal).
chrom loc.start loc.end num.mark seg.mean
chr1 126901 336305 20 -0.2205
chr1 566191 569388 3 1.2087
chr1 653310 2338123 1505 -0.1378
chr1 2338223 16057066 5079 -0.19
chr1 16057166 16258373 168 -0.1205
chr1 16258673 16258973 4 -1.2245
chr1 16259073 17012168 579 -0.1526
chr1 17012268 17273478 48 0.0673
chr1 17282515 26109165 4152 -0.1866
I am trying to do this using the mergeSegments.pl package and am getting the following message:
Use of uninitialized value $input in <handle> at ../../apps/mergeSegments.pl line 446.
readline() on unopened filehandle at ../../apps/mergeSegments.pl line 446.
Can't use an undefined value as a symbol reference at ../../apps/mergeSegments.pl line 456.
I am trying to figure out what I am doing wrong. Initially, I figured that my file was in the wrong format. The mergeSegments specifies that the input should be:
"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."
My file doesn't have an ID, bstat, pval, lcl, or ucl and I'm not even sure how I would generate these if indeed this was the issue. Any help would be greatly appreciated. Thank you very much.