Dear all, I am using CNVkit to analyse exome sequencing data (germline samples) in order to find new copy number variants. For the pipeline analysis I followed all the found suggestions for germline samples and here are the steps:

1) create a reference using all samples

cnvkit.py batch --normal ALL_BAM/*.bam --targets Exome_SureSelect_QXTV7_forCNVkit.bed --fasta hs37d5.fa --access access-5k-mappable.hg19.bed --output-reference reference.cnn

2) batch command using the previously created reference

cnvkit.py batch ALL_BAM/*.bam -r reference.cnn -d results/

3) add ci column

cd results/
for i in *.cnr ; do cnvkit.py segmetrics -s `basename ${i%%.cnr}`.cn{s,r} --ci ; done

4) call command

for i in *segmetrics* ; do cnvkit.py call $i --filter ci -m clonal --center mode -o call_cnvkit/`basename ${i%%segmetrics*}`.call.cns; done

5) cnv_ztest

for i in *.cnr; do cnv_ztest.py $i -t -s call_cnvkit/`basename ${i%%.cnr}..call.cns` -o cnv_ztest/`basename ${i%%.cnr}`.ztest.cnr; done

I am now looking at cnv_ztest results but I am not understanding log2 values reported in the file because they have quite negative values in all samples (like between -21 and -8). Is there something I am missing? Or probably is there an error in my pipeline? I also had a look at this thread but because I am using germline samples I didn't use the --drop-low-coverage as suggested. Do you have any idea about what is going wrong? Thanks in advance!

Stefania