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Error When Running The Varscan Mergesegments.Pl Tool

I generated the correct columns and the mergeSegments.pl still fails:

perl ../../apps/mergeSegments.pl outp.file
Use of uninitialized value $input in 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.

This is the file format: ID chrom loc.start loc.end num.mark seg.mean bstat pval lcl ucl

Sample.1 chr1 126901 336305 20 -0.2205 7.35726563517599 3.50306367498813e-12 336305 336305
Sample.1 chr1 566191 569388 3 1.2087 8.08753912963223 1.21687750240143e-13 569388 569388
Sample.1 chr1 653310 2338123 1505 -0.1378 6.06563083831769 2.6260014877838e-07 2234624 2446703
Sample.1 chr1 2338223 16057066 5079 -0.19 3.1268048900692 0.149143434568713 15904118 16174570

Any help would be greatly appreciated. Thanks.

varscan copynumber cnv exome sequencing
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updated by Biostar Biostar • written by sousuffer • sousuffer

2 answers

You need to provide the script a ref-arm-sizes file. See the documentation.

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written by dankoboldt • dankoboldt

Is anyone able to assist me with this? Thanks.

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written by sousuffer • sousuffer

please don't add this as an answer it only hurts your chances since now people think this question has been answered. Dan Koboldt the author of Varscan usually swoops in every other week and answers questions on this, but make sure to delete your answer,.

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written by Istvan Albert Istvan Albert

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