Error When Running The Varscan Mergesegments.Pl Tool
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Entering edit mode
8.6 years ago
sousuffer ▴ 20

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 • 2.1k views
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Entering edit mode
8.1 years ago
dankoboldt ▴ 140

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

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