Hi there, I'm using Varscan2 CNV pipeline to deal with my exome data, it works fine until the last step which needed a perl script "mergeSegment.pl". my command is like:
perl mergeSegments.pl --ref-arm-sizes ./chr_arm_coordinate.txt ./blahblahblah.copynumber
The copynumber file was generated by R package DNAcopy, with 10 columns as mergeSegment.pl requires, here's the format:
ID chrom loc.start loc.end num.mark seg.mean bstat pval lcl ucl
MetS6 1 762098 1635855 1040 -0.8484 7.868273154 6.30E-13 1635609 1646602
MetS6 1 1645759 1654150 11 -1.402 6.795998163 3.43E-10 1647851 1663751
MetS6 1 1663751 1690511 33 -0.8588 4.428916611 0.000268018 1688073 1721814
Then I got error below:
Use of uninitialized value $stats{"num_merged_events"} in array element at mergeSegments.pl line 182, <GEN1> line 3.
Use of uninitialized value in split at mergeSegments.pl line 255.
Use of uninitialized value $chrom_size in division (/) at mergeSegments.pl line 271.
Illegal division by zero at mergeSegments.pl line 271.
Any suggestions would be greatly appreciated, Thanks!
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written
by
Conan •
5 answers
It appears that your CBS output file differs slightly in structure from the output expected by mergeSegments.pl (see line 134):
my ($id, $sample, $chrom, $chr_start, $chr_stop, $num_mark, $seg_mean, $bstat, $p_value, $lcl, $ucl) = split(/\s+/, $line);
Your line does not appear to have both ID and sample columns. Thus if you remove one of those variables in the split command, it should work for you.
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written
by
dankoboldt •
Does this solve your problem? Questions About Mergesegment.Pl
I am getting the same error, so I simply added the sample column: Sample input:
ID sample chrom loc.start loc.end num.mark seg.mean bstat pval lcl ucl
Sample.1 ABC chr1 801880 1580650 192 23.6745 14.52182109 1.32E-45 1580650 1581021
But I still get the errors: Use of uninitialized value $stats{"num_merged_events"} in array element at ../../mergeSegments.pl line 182, <gen1> line 184. Use of uninitialized value in split at ../../mergeSegments.pl line 255. Use of uninitialized value $chrom_size in division (/) at ../../mergeSegments.pl line 271. Illegal division by zero at ../../mergeSegments.pl line 271.
The ----ref-arm-sizes file is in the format: chr1 0 125000000 p chr1 125000000 249250621 q
Any help is appreciated! ~Rini
I had the same problem, then i removed $sample from line 134 as he said, which initially looks like this
my ($id, $sample, $chrom, $chr_start, $chr_stop, $num_mark, $seg_mean, $bstat, $p_value, $lcl, $ucl) = split(/\s+/, $line);
Still gives this error
Use of uninitialized value $stats{"num_merged_events"} in array element at /home.../mergeSegments.pl line 182, <GEN1> line 3.
Also gives some results just below the error
You may want to see this post also, it is helpfull
http://sourceforge.net/p/varscan/discussion/1073558/thread/96c8dea8/?limit=25#3c10
Hi
I'm currently having the exact same problem with mergeSegments.pl
Use of uninitialized value $stats{"num_merged_events"} in array element at mergeSegments.pl line 182, <gen1> line 2. Use of uninitialized value in split at mergeSegments.pl line 255. Use of uninitialized value $chrom_size in division (/) at mergeSegments.pl line 271. Illegal division by zero at mergeSegments.pl line 271.
Did you resolve this problem? Also, I am right in thinking the input file should not have a header.
Best wishes
this post might be helpful.
- remove chromosome from your segmentation file that are not in your chr_arm length file.
http://sourceforge.net/p/varscan/discussion/1073559/thread/996c2875/?limit=25#68b2
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