之前做SSR标记和简化测序都是用的桌面化的TASSEL进行运算，对于做关联分析的初学者非常简单，十分好入门。但是关于命令行的操作就要麻烦一些，但是运算起来不像GAPIT那样消耗大量的内存，下面做一些简单的示例。

安装

Install Java JDK8.0

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#下载
wget http://download.oracle.com/otn-pub/java/jdk/8u112-b15/jdk-8u112-linux-x64.rpm
#安装
rpm -ivhc jdk-8u112-linux-x64.rpm
#测试安装
java -vsrsion
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[root@lilibei java]# java -version
java version "1.8.0_112"
Java(TM) SE Runtime Environment (build 1.8.0_112-b15)
Java HotSpot(TM) 64-Bit Server VM (build 25.112-b15, mixed mode)
  • 更改环境变量
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vim /etc/profile

按照如下添加

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JAVA_HOME=/usr/java/jdk1.8.0
JRE_HOME=/usr/java/jdk1.8.0/jre
PATH=$PATH:$JAVA_HOME/bin:$JRE_HOME/bin
CLASSPATH=.:$JAVA_HOME/lib/dt.jar:$JAVA_HOME/lib/tools.jar:$JRE_HOME/lib
export JAVA_HOME JRE_HOME PATH CLASSPATH
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#编辑完后执行脚本
source /etc/profile
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[root@cricaas java]# echo $PATH
/usr/lib64/qt-3.3/bin:/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/git/bin:/home/lilibei/bin:/root/bin:/usr/local/git/bin:/home/lilibei/bin:/usr/java/jdk1.8.0/bin:/usr/java/jdk1.8.0/jre/bin
[root@cricaas java]# echo $JAVA_HOME
/usr/java/jdk1.8.0

Install TASSEL

TASSEL的安装简单，操作如下：

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#github clone
git clone https://bitbucket.org/tasseladmin/tassel-5-standalone.git
cd tassel-5-standalone

使用说明

示例文件存放路径

/home/lilibei/tassel-5-standalone/TASSELTutorialData/data/

kinship矩阵

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#适合小数据集，重测序数据需要更改内存配置参数
./run_pipeline.pl -fork1 -h TASSELTutorialData/data/mdp_genotype.hmp.txt -ck -export kinship.txt

LD分析

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#绘制LD连锁图，很难看，可以使用hapview或者LDheatmap
./run_pipeline.pl -fork1 -h TASSELTutorialData/data/mdp_genotype.hmp.txt -ld -ldd png -o chr_5000sites_ld.png
#计算LD
./run_pipeline.pl -fork1 -h TASSELTutorialData/data/mdp_genotype.hmp.txt -ld -export LD_5000sites

提取染色体

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#提取每条染色体
./run_pipeline.pl -fork1 -h TASSELTutorialData/data/mdp_genotype.hmp.txt -separate  -export chromosome
#提取1和3号染色体
./run_pipeline.pl -fork1 -h TASSELTutorialData/data/mdp_genotype.hmp.txt -separate 1,3  -export chromosome

MLM分析

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./run_pipeline.pl -fork1 -h TASSELTutorialData/data/mdp_genotype.hmp.txt -filterAlign -filterAlignMinFreq 0.05 -fork2 -r TASSELTutorialData/data/mdp_traits.txt -fork3 -q TASSELTutorialData/data/mdp_population_structure.txt -excludeLastTrait -fork4 -k TASSELTutorialData/data/mdp_kinship.txt -combine5 -input1 -input2 -input3 -intersect -combine6 -input5 -input4 -mlm -export lilibei -runfork1 -runfork2 -runfork3 -runfork4

格式转化

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#vcf -> hmp
/home/lilibei/tassel-5-standalone/run_pipeline.pl -Xms512m -Xmx10g -fork1 -vcf 355-5W.vcf -export 355-5W-hmp -exportType HapmapDiploid
#Type can be Hapmap, HapmapDiploid,
#HDF5, VCF, Plink, Phylip_Seq, Phylip_Inter,
#Fasta

参考资料

1.TASSEL5.0命令行官方使用手册
2.https://bytebucket.org/tasseladmin/tassel-5-source/wiki/docs/Tassel_Pipeline_Tutorial20110511.pdf