Hi Biostars Users,
I would like to know if you have encountered this issue while working with CONTRA tool for detecting CNVs in targeted NGS.
In fact, my analysis is "stopping" at the binning process with no error message, I have checked all the required arguments and they seem to be ok :
contra apple$ python contra.py --target ngs1_probes.bed --test cic04668.bam --control baseline_ngs1.bed --bed --fasta human_ref.fasta --outFolder ~/contrases target : ngs1_probes.bed test : cic04668.bam control : baseline_ngs1.bed fasta : human_ref.fasta outfolder : /Users/apple/contrases numBin :  minreaddepth : 10 minNBases : 10 sam : False pval : 0.05 sampleName : No-SampleName nomultimapped : False plot : False bedInput : True minExon : 2000 largeDeletion : False Creating Output Folder : Done. Converting TEST Sample... DEBUG 123 genomeCoverageBed -ibam cic04668.bam -bga -g /Users/apple/contrases/buf/sample.Genome Converting CONTROL Sample... Getting targeted regions DOC... chr1 chr10 chr11 chr12 chr14 chr15 chr16 chr17 chr19 chr2 chr20 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chrX Targeted regions pre-processing: Done Getting targeted regions DOC... chr1 chr10 chr11 chr12 chr14 chr15 chr16 chr17 chr19 chr2 chr20 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chrX Targeted regions pre-processing: Done Test file read depth = 97323185 Control file read depth = 98289477 Pre-processing Completed. Getting the Log Ratio Binning....
Do you have any idea why?
Thank you for your help