April 2022
Beginner to intermediate
486 pages
10h 22m
Chinese
Content preview from 云端基因组学
Become an O’Reilly member and get unlimited access to this title plus top books and audiobooks from O’Reilly and nearly 200 top publishers, thousands of courses curated by job role, 150+ live events each month,
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.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.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.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.
用
GATK
最佳实践发现体细胞变异
｜
217
你可以用
gsutil
工具从你的虚拟机复制
GATK
工具输出的图表到你的谷歌桶，然
后从
GCP
平台控制台查看（或下载）它们。如需温习这块知识，请见第
4
章。下面
命令是在你虚拟机（学习第
4
章时，已安装和配置好
gsutil
工具），而非在其中运
行
gatk
命令的
Docker
容器运行。
gstuil
命令将图表上传到你在该示例中指定的桶
（
my-bucket
）：
$ export BUCKET="gs://my-bucket"
$ gsutil -m cp -R sandbox/cna_plots $BUCKET/somatic-sandbox/
这些图放到书中，难以看真切，但你自己生成的图，放大之后，应该能够看到经第
二轮处理，数值的范围比第一轮处理结果更紧凑，这表明从一步到另一步，结果有
所改进。无论如何，我们认可这些数值较图
7-8
的原读段计数表现出更高的精度，
并且我们已看到一些可能的
CNA
。
7.3.4
连接片段并识别
CNA
我们已得到去噪后的拷贝率，只需准确识别哪些区域给出存在
CNA
的证据。为此
我们连接拷贝率相似的相邻片段。接着我们应该就能确定哪些片段的总拷贝率相对
于其余片段存在扩增或删除。
我们用
ModelSegments
工具来完成该分析。该工具用高斯内核二分片段连接算法来
执行多维内核片段连接操作。
# gatk ModelSegments \
--denoised-copy-ratios sandbox/hcc1143_T_clean.denoisedCR.tsv ...
Become an O’Reilly member and get unlimited access to this title plus top books and audiobooks from O’Reilly and nearly 200 top publishers, thousands of courses curated by job role, 150+ live events each month,
and much more.
Read now
Unlock full access
More than 5,000 organizations count on O’Reilly
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.