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.RData
.RData
 
 
GenomeWideSNP_6.hg18.cnv_defs
GenomeWideSNP_6.hg18.cnv_defs
 
 
GenomeWideSNP_6.hg38.cnv_defs
GenomeWideSNP_6.hg38.cnv_defs
 
 
README
README
 
 
ccnvr
ccnvr
 
 
example.canary_calls
example.canary_calls
 
 
example.hmm
example.hmm
 
 
example.pfb
example.pfb
 
 
father.txt
father.txt
 
 
inputlist
inputlist
 
 
list.compcall
list.compcall
 
 
list.compdup
list.compdup
 
 
mother.txt
mother.txt
 
 
offspring.txt
offspring.txt
 
 
runex.pl
runex.pl
 
 

README

This directory contains some example files to run PennCNV, assuming that PennCNV is already installed in the system and that the executables are already in the system PATH environmental variable.

The runex.pl script can be issued to run sample sessions:

The user can run these programs sequentially:

perl runex.pl 1

perl runex.pl 2
	
perl runex.pl 3

......

perl runex.pl 16

If PennCNV is not set up in the PATH environmental variable, the user need to add '-path_detect_cnv ../detect_cnv.pl' argument to the above commands.

If there is any problem running the examples, or if the output files differ from those in the output_expected/ directory, it may indcate that PennCNV is not installed correctly.