YaqingLiu
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CNVkit
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Infer and visualize copy number from high-throughput DNA sequencing data.
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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

Input

{
	"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.