Question About Mergesegment.Pl In Varscan 2

Question

[Conan]

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!

Answer 1

[dankoboldt]

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.

Answer 2

[Chris Miller]

Does this solve your problem? Questions About Mergesegment.Pl

[Conan]

Thank you for your instant reply Chris, I actually used ref-arm-sizes file that post recommended, and got the error above.

Answer 3

[P]

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

Answer 4

[suleymanvural]

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

Answer 5

[matthew.1.davies]

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

[CHANG]

this post might be helpful.

1. 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