April 2022
Beginner to intermediate
486 pages
10h 22m
Chinese
Content preview from 云端基因组学
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126
｜
第
5
章
GATK
工具名几乎都枯燥乏味（
Funcotator
可能是个例外），大多工具名可
以表达清楚工具的用途，为工具命名理应做到这一点。该工具集包含
200
多
种工具，工具名如只顾讨人喜欢却丝毫不能说明工具的用途，用户会疯。
请注意，该工具集完全开源，其公开发行版的某些工具，仍处于活跃的开发或实验
阶段，这些工具在其文档中有相应提示，并且其输出日志通常含免责声明。
GATK
工具主要设计成在命令行使用。在各种应用场景，你甚至不用直接运行命令
就能使用它们，例如，将工具或工作流脚本封装为图形用户界面，通过该界面使用
命令。实际上，
GATK
大多数大规模和例行使用，通常都用工作流完成，详见第
8
章。
鉴于你刚学着使用该工具集，我们决定剥掉所有这些外壳，直接在终端运行单个命
令以展示其基本用法，并教你用自定义工具处理数据。
5.1.1
运行要求
GATK
用
Java
语言开发，只要机器安装合适
Java
版本（写作本书时，安装
JRE
或
JDK 1.8
即可），几乎都可以运行，但微软
Windows
系统除外，因为
GATK
不支
持该系统。
GATK
不需要传统意义上的安装操作，如要用
GATK
，最简单方式是：
下载
GATK
包，将其放到硬盘（或服务器文件系统）合适目录。你可以根据需要将
GATK wrapper script
加到系统路径。
然而，
GATK
的某些工具（尤其是使用了时髦机器学习库的）需要额外的
R
和（或）
Python
依赖，其安装就相当痛苦。这些依赖可能与其他工具的要求相冲突，这点着
实令人苦恼。例如，你正在用的
GATK
版本依赖 ...
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O’Reilly covers everything we've got, with content to help us build a world-class technology community, upgrade the capabilities and competencies of our teams, and improve overall team performance as well as their engagement.Julian F.
I wanted to learn C and C++, but it didn't click for me until I picked up an O'Reilly book. When I went on the O’Reilly platform, I was astonished to find all the books there, plus live events and sandboxes so you could play around with the technology.Addison B.
I’ve been on the O’Reilly platform for more than eight years. I use a couple of learning platforms, but I'm on O'Reilly more than anybody else. When you're there, you start learning. I'm never disappointed.Amir M.
I'm always learning. So when I got on to O'Reilly, I was like a kid in a candy store. There are playlists. There are answers. There's on-demand training. It's worth its weight in gold, in terms of what it allows me to do.