April 2022
Beginner to intermediate
486 pages
10h 22m
Chinese
Content preview from 云端基因组学
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Jupyter Notebooks
中的交互式分析
｜
379
提供一种更完整和无缝的体验，当时我们在一台虚拟机运行
GATK
命令，接着在桌
面版
IGV
浏览器可视化其结果。我们让你体验该过程，一则我们是悲观主义者，二
则我们想给你机会夯实基本技能。练习过程，你有机会熟悉云计算基本组件，这块
内容应有助于你理解在笔记本运行工作流或从事其他工作时，背后发生了什么。经
过这一学习过程，你再教学、测试或解决问题，就会更加欣赏使用笔记本的便捷之处。
为达到该目的，我们将重做第
5
章的练习，以便你集中精力研究如何做这些工作而
不必把时间放在理解这些分析任务上。
12.4.1
运行
GATK
基本命令：
HaplotypeCaller
让我们开始在本书一直在用的同一样本上运行
HaplotypeCaller
工具。你应认识该
命令，因为我们几乎一字不差将其从第
5
章复制过来：
In [33] ! gatk HaplotypeCaller \
-R {GERM_DATA}/ref/ref.fasta \
-I {GERM_DATA}/bams/mother.bam \
-O sandbox/mother_variants.200k.vcf.gz \
-L 20:10,000,000-10,200,000
该命令的运行方式较第
5
章有何不同？现在你应认识
GATK
命令前的英文叹号，它
告知笔记本不要用
Python
解释器解析该命令，而是将其作为
shell
命令执行。该命
令引用文件路径变量的方式也有点不同，因为我们使用大括号而非之前的 ...
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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.