Question: Question: Question About Mergesegment.Pl In Varscan 2
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gravatar for luxin7091012
5.6 years ago by
luxin70910120 wrote:

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.

two questions: 1: Can somebody give me a correct arm size format.(I use a format gived by "Questions about mergeSegment.pl"like 1 0 125000000 p 1 125000000 249250621 q I got error too ) 2: Can somebody who succeeded run this perl script share all your input and output. If the author can give some detail format, I will be greatly appreciate. Thanks very much for any help.

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ADD COMMENTlink written 5.6 years ago by luxin70910120

Do a search on Biostar for "mergeSegment" I'm almost positive that this has been asked and answered before.

ADD REPLYlink written 5.6 years ago by Chris Miller20k
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