Hi I am using the CNVnator tool for copy number variation.
My Coomand is these
cnvnator -root out.root -genome GCA_000003055.5_Bos_taurus_UMD_3.1.1_genomic.fna -chrom GK000001.2 -unique -tree mem_snp_against_ref.bam
cnvnator -root out.root -genome GCA_000003055.5_Bos_taurus_UMD_3.1.1_genomic.fna -chrom GK000001.2 -his 100
cnvnator -root out.root -genome GCA_000003055.5_Bos_taurus_UMD_3.1.1_genomic.fna -chrom GK000001.2 -stat 100
After Step 3 output I got Making statistics for GK000001.2 ... Average RD per bin (1-22) is 10.7382 +- 4.93978 (before GC correction) Warning in <fit>: Fit data is empty Warning in <fit>: Fit data is empty Average RD per bin (X,Y) is 0 +- 0 (before GC correction) Correcting counts by GC-content for 'GK000001.2' ... Making statistics for GK000001.2 after GC correction ... Average RD per bin (1-22) is 10.9311 +- 5.46794 (after GC correction) Warning in <fit>: Fit data is empty Warning in <fit>: Fit data is empty Average RD per bin (X,Y) is 0 +- 0 (after GC correction)
Its difficult to understand that it is the real error or just the warning message. and if this is the error what is it and how to correct that.
Please help me.....
