Somatic and germline CNV calling from WGS data

[anitha-ravichandran]

Hi,
I am trying to call somatic and germline CNV from WGS data. I have tumor and its adjacent normal samples (For somatic CNV call). And Tumor and its adjacent normal samples, only tumor samples without the adjacent normal sample (For germline CNV call). I dont have complete disease free normal samples. What is the step by step procedure for this. I have read the tutorial but I could not understrand clearly, like how the target and anti-target is generated for WGS. how the reference (.cnn) file is created, using pooled adjacent normal or for each sample to create the .cnn file.
Example samples:
Tumor Normal
ST1 SN1
ST2 SN2
ST3 SN3
ST4 -
ST5 -

[SevenTea7]

Hello,
I have a problem when running cnvkit.py, cannot import name 'Int64Index' from 'pandas'. Could you please share your pandas and cnvkit versions with me? Thank you.
Yang

[anitha-ravichandran]

I have downloaded the cnvkit using docker pull. Here is the command that I have used.
"docker pull etal/cnvkit"
"docker run -it etal/cnvkit