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.
202
｜
第
7
章
7.2.3
在肿瘤—正常组织配对上运行
Mutect2
工具
掌握
PoN
队列创建方法之后，我们继续学习本节主要内容，在肿瘤—正常组织配
对上运行
Mutect2
工具，所用
PoN
队列文件我们已建好，含
40
个公开可用的正常
样本，这些样本来自千人基因组计划。与第
6
章相同，我们将在我们信任的虚拟
机的
GATK
容器内开展该工作，因此如你的虚拟机还没开机请开机，并按第
5
章
我们教你的步骤启动
GATK
容器。不同的是，我们的工作目录为
/home/book/data/
somatic
，并且我们需另建一沙盒：
# cd /home/book/data/somatic
# mkdir sandbox
我们在肿瘤—正常组织配对上一起运行
Mutect2
命令，用参数
-normal
指定正常样
本的名称（编码到
BAM
文件的
SM
标记）。我们分别用参数
-pon
和
--germline-
resource
提供
PoN
队列文件和
gnomAD
种系资源。我们还指定片段（用
-L
参数指
定片段列表文件），因为我们正在操作外显子组数据：
# gatk Mutect2 \
-R ref/Homo_sapiens_assembly38.fasta \
-I bams/tumor.bam \
-I bams/normal.bam \
-normal HCC1143_normal \
-L resources/chr17plus.interval_list \
-pon resources/chr17_m2pon.vcf.gz ...
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.