I have a little problem with CNVkit.
I normally use cnvkit to calculate CNV in a whole exome panel and I have no problems and I have a good results. But now I'm trying to calculate them in a smaller panel (50 genes). The commands Ihave used are the same but with a different bed file.
cnvkit.py batch sample_sorted_ND.bam --normal *sorted_ND.bam -t my-targets.bed --fasta hg19_ref_genome.fa --access data/access-5kb-mappable.hg19.bed --output-reference my_Mreference.cnn --output-dir example1
The problem is that, when I look at the log2 in the cnr file, the only regions I have out of range are BRCA1_14 and BRCA_13, which is the deletion that there really is.
chr17 41228504 41228631 427_15619_672(BRCA1)_14 142535 -0.540179 0.629573 chr17 41231350 41231416 427_15618_672(BRCA1)_13 119045 -0.672668 0.552469
But in the diagram comes out many genes (most of the genes in the panel but not BRCA1), Why? Should not only go uot these regions? I am doing something wrong? I must add something else on the command line?
Other question is that the deph column is not correct since it does not always recognize decimals.
Some one can help me?