CNVkit/README.md

# CNVkit

> Author： Yaqing Liu
>
> E-mail：yaqing.liu@outlook.com
>

## Install

```
# activate choppy environment
open-choppy-env
# install app
choppy install YaqingLiu/CNVkit
```

## Copy number calling pipeline
![image](https://cnvkit.readthedocs.io/en/stable/_images/workflow.png)

## Input
```json
{
	"tumor_bam": [
          "oss://choppy-cromwell-result/...bam",
          "oss://choppy-cromwell-result/...bam",
          "oss://choppy-cromwell-result/...bam"
	],
	"tumor_bai": [
          "oss://choppy-cromwell-result/...bai",
          "oss://choppy-cromwell-result/...bai",
          "oss://choppy-cromwell-result/...bai"
	],
	"normal_bam": [
          "oss://choppy-cromwell-result/...bam",
          "oss://choppy-cromwell-result/...bam",
          "oss://choppy-cromwell-result/...bam"
	],
	"normal_bai": [
          "oss://choppy-cromwell-result/...bai",
          "oss://choppy-cromwell-result/...bai",
          "oss://choppy-cromwell-result/...bai"
    ],
	"sample_id": "..."
}
```
#### Output
A segment file and some intermediate *.cnn/cns will be generated, and the segment file can be imported into IGV.