Empty output file ".bam_CNVS"

[ZKai0801]

Hi Dr. Boeva,

I encountered some difficulties during finding CNVs using control-freec. The process of running freec did not generate any error message, however, the output file ".bam_CNVs" was empty. I have already test my data on other software and can confirm that there are plenty of CNVs in my data. So. I'm wondering why this happened and hope you may be able to give me some help.

Here is my configure file:

[general]
chrLenFile = /public/home/kai/test_kai/NGS_cnv/freec_test/hg19.len.txt
window = 3000
step = 1000
ploidy = 2
outputDir = /public/home/kai/test_kai/NGS_cnv/freec_test/test3/output
samtools = /public/home/kai/softwares/samtools/samtools

[sample]
mateFile = /public/home/kai/test_kai/NGS_cnv/cnvkit_test/testdata/tumour1.bam
inputFormat = BAM
matesOrientation = 0

[control]
mateFile = /public/home/kai/test_kai/NGS_cnv/cnvkit_test/testdata/control.bam
inputFormat = BAM
matesOrientation = 0

[target]
captureRegions = /public/home/kai/test_kai/NGS_cnv/cnvkit_test/testdata/YJ.bed

[valeu]

Most likely chromosome names in YJ.bed, control.bam and hg19.len.txt do not match. To see what is going on exactly, one need to have a full output of FREEC into the command line using your config file.