CNVkit/README.md

# CNVkit

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

CNVkit is a Python library and command-line software toolkit to infer and visualize copy number from high-throughput DNA sequencing data. It is designed for use with hybrid capture, including both whole-exome and custom target panels, and short-read sequencing platforms such as Illumina and Ion Torrent.

Official document: https://cnvkit.readthedocs.io/en/stable/index.html
## 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": "...",
    "method": "...",
    "reference": "..." # this parameter is optional
}
```
***Note***
```shell
-m {hybrid,amplicon,wgs}, --seq-method {hybrid,amplicon,wgs}, --method {hybrid,amplicon,wgs}
        Sequencing assay type: hybridization capture
        ('hybrid'), targeted amplicon sequencing
        ('amplicon'), or whole genome sequencing ('wgs').
        Determines whether and how to use antitarget bins.

To reuse an existing reference or create a new :
-r REFERENCE, --reference REFERENCE
        Copy number reference file (.cnn).
--output-reference FILENAME
        Output filename/path for the new reference file
        being created. (If given, ignores the 
        -o/--output-dir option and will write the file to
        the given path. Otherwise, "reference.cnn" will
        be created in the current directory or specified
        output directory.)
```
## Output
1. *.cnn/cns of each sample.
2. A whole-genome copy ratio profile as a PDF scatter plot.
3. An ideogram of copy ratios on chromosomes as a PDF.
4. A segment file which can be imported into IGV.