I am working with PennCNV software to analyze 300 samples (chickens) and I used below command for this analysis:
./detect_cnv.pl -test -hmm lib/hh550.hmm -pfb lib/hh550.hg18.pfb sample1.txt sample2.txt sample3.txt -log sampleall.adjusted.log -out sampleall.adjusted.rawcnv -gcmodel hh550.hg18.gcmodel
but the software does not report any CNVs for a large number of samples (125 samples) without any errors or warnings.
For example, one of these samples is sample1.txt , which after running, the software gives the following notices but the output file is empty :
NOTICE: All program notification/warning messages that appear in STDERR will be also written to log file sampleall.adjusted.log NOTICE: Reading marker coordinates and population frequency of B allele (PFB) from out.pfb ... Done with 51348 records (3980 records in chr W,0,Z,LGE64,LGE22C19W28_E50C23 were discarded) NOTICE: Reading LRR and BAF values for from sample1.txt ... Done with 51348 records in 29 chromosomes (3981 records are discarded due to lack of PFB information for the markers) NOTICE: Adjusting LRR by GC model: WF changes from -0.0105 to 0.0111, GCWF changes from -0.0024 to 0.0001</code> NOTICE: Data from chromosome 32 will not be used in analysis NOTICE: Median-adjusting LRR values for all autosome markers from sample1.txt by 0.0039 NOTICE: Median-adjusting BAF values for all autosome markers from sample1.txt by -0.0303 NOTICE: quality summary for sample1.txt: LRR_mean=-0.0063 LRR_median=0.0000 LRR_SD=0.1207 BAF_mean=0.4980 BAF_median=0.5000 BAF_SD=0.0399 BAF_DRIFT=0.000000 WF=0.0111 GCWF=0.0001
I hope you help me