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WGLab / PennCNV

Copy number vaiation detection from SNP arrays
http://penncnv.openbioinformatics.org
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clean_cnv.pl output - Empty file #79

Closed mrinalmishra closed 2 years ago

mrinalmishra commented 2 years ago

Hello,

I have a penncnv output file and I am trying to use clean_cnv.pl to merge adjacent cnv calls. However, whenever I am running the clean_cnv.pl command, it is not throwing any error but there is nothing in the output file i.e. the output file is created but it is empty.

Here is the command line I am running - clean_cnv.pl combineseq input_cnv_file.rawcnv --signalfile 1M_snppos.txt --output combine_cnv.rawcnv.

Also, I am attaching subsection of my input and signalfile so that you can have a look snppos.txt input_cnv_file.txt .

mrinalmishra commented 2 years ago

The problem is resolved. I was doing a stupid mistake. I was using 'combineseq', instead of 'combineseg'.