pegi3s/gatk-4
pegi3s
GATK 4 (https://gatk.broadinstitute.org/hc/en-us) docker image.
下载次数: 0状态：社区镜像维护者：pegi3s仓库类型：镜像最近更新：2 年前
让 AI 帮你使用轩辕镜像？ · 展开查看说明 · 点击收起说明
如果你使用 DeepSeek、元宝 AI、Copilot、ChatGPT 等 AI 工具，协助配置轩辕镜像、编写 docker pull 命令、修改 Docker Compose 镜像地址、配置镜像加速、排查镜像拉取失败、分析报错日志等问题，请先让 AI 阅读并遵守轩辕镜像的规则文档。
只需在 AI 对话中先发送下面这句话即可：
请先完整阅读并严格遵守以下文档中的全部规则与要求：
https://xuanyuan.cloud/agents.md
在未充分阅读并理解该文档前，不要生成任何命令、配置、修改建议、故障排查方案或技术回答。后续所有输出都必须严格以该文档中的规范为最高优先级执行。查看 agents.md 用法指南与完整示范。国内用户首推 元宝 AI、DeepSeek 的深度思考模式，不推荐豆包 AI；Cursor 等编辑器可在对话 @ 该链接，或加入 User Rules。 若 AI 无法访问外链，可 打开说明文档 复制全文粘贴。文档会随站点更新，复制内容可能过期，建议定期检查。
This image belongs to a larger project called Bioinformatics Docker Images Project (http://pegi3s.github.io/dockerfiles)
(Please note that the original software licenses still apply)
This image facilitates the usage of https://gatk.broadinstitute.org/hc/en-us, the industry standard for identifying SNPs and indels in germline DNA and RNAseq data. Its scope is now expanding to include somatic short variant calling, and to tackle copy number (CNV) and structural variation (SV). In addition to the variant callers themselves, the GATK also includes many utilities to perform related tasks such as processing and quality control of high-throughput sequencing data, and bundles the popular Picard toolkit.
To see GATK 4 available tools, just run docker run --rm pegi3s/gatk-4:4.1.4.1 gatk --list. Please note that GATK 4 does not include some tools that are included in https://hub.docker.com/r/pegi3s/gatk-3.
To obtain the help of a particular tool, you just need to run: docker run --rm pegi3s/gatk-4:4.1.4.1 gatk <tools> --help (e.g. docker run --rm pegi3s/gatk-4:4.1.4.1 gatk SortVcf --help)
Using the GATK 4 image in Linux
You should adapt and run the following command: docker run --rm -v /your/data/dir:/data pegi3s/gatk-4:4.1.4.1 gatk <tools> <options>
In this command, you should replace:
/your/data/dirto point to the directory that contains the input files you want to analyze.<tools>to the name of theGATK 4tool you want to use.<options>with the specific options of theGATK 4tool. These options will include the input/output files, which should be referenced under/data/.
For instance, to sort a VCF file using GATK 4, you should run: docker run --rm -v /your/data/dir:/data pegi3s/gatk-4:4.1.4.1 gatk SortVcf -I /data/test.recode.vcf -O /data/test_sorted.recode.vcf
Test data
To test the previous command, the VCF file used is available here.
镜像拉取方式
您可以使用以下命令拉取该镜像。请将 <标签> 替换为具体的标签版本。如需查看所有可用标签版本，请访问 标签列表页面。
DockerHub 原生拉取命令
docker pull pegi3s/gatk-4:<标签>
镜像拉取常见问题
功能
错误码
用户好评
来自真实用户的反馈，见证轩辕镜像的优质服务
oldzhang
运维工程师
Linux服务器
5
"Docker访问体验非常流畅，大镜像也能快速完成下载。"