April 2022
Beginner to intermediate
486 pages
10h 22m
Chinese
Content preview from 云端基因组学
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380
｜
第
12
章
运行大多数命令；这种方法在你的虚拟机上应该能正常工作。然而，当时我们认为
过早介绍这些内容可能令你无所适从，因为你很可能是初次体验云服务。因此我们
只教你在本地文件上运行命令，期望这段学习经历足以让你熟悉云服务。我们现在
提出这种新方法，为的是即使你选择回到虚拟机环境工作，也知道自己仍可以利用
数据流功能。并且你可能还记得，我们第
10
章讨论优化时讲过，该方法亦适用于
WDL
工作流场景。
当你运行命令，你应该会看到笔记本将日志输出到刚运行的单元格下面。笔记本将
分析的所有相关信息放到一处，这种体验真的很好，这是
Jupyter
设计理念的一大优
点。然而美中不足的是，如工具的输出特别长（如
GATK
偶尔会这样），笔记本中
的日志就可能长达数页。遇到该情况，我们可在
Markdown
单元格使用清晰的小节
标题，将分析工作拆成不同部分。这对工作帮助很大，特别是结合使用笔记本控件，
自动创建目录和侧边栏导航按钮。
HaplotypeCaller
工具运行完，我们查看沙盒内容，确定命令成功创建变异识别
VCF
文件：
In [34] ! ls sandbox/
是的，该文件及其索引文件乖乖地躺在这里。我们接下来用
IGV
浏览器查看它。
12.4.2
加载数据（
BAM
和
VCF
）到
IGV
浏览器
假如我们要在笔记本用
IGV
浏览器打开
VCF
文件，并用肉眼检查、比较它和
BAM
文件的不同。我们就可以用前面创建的
IGV
浏览器，探究不同
BAM
文件，但这是
一个独立练习，其目的偏离主线，而且我们太懒，不想滚动很多页，因此我们新建
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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.