GWAS分析

命令行中tassel的使用

2018-08-16  本文已影响202人  灵动的小猪
cd 
wget -c https://bitbucket.org/tasseladmin/tassel-5-standalone/get/5f8d2852556a.zip
zip 5f8d2852556a.zip
mv tasseladmin-tassel-5-standalone-5f8d2852556a/ tassel/
echo export "PATH=/tassel/tassel:$PATH" >>.bashrc
run_pipeline.pl -ListPlugins
run_pipeline.pl -<plugin_name> 
run_pipeline.pl -ListPlugins
run_pipeline.pl -importGuess maize.hmp.txt -KinshipPlugin -method Centered_IBS -endPlugin -ExportPlugin -saveAs maize_kinship.txt -format SqrMatrix
管道可以由多个管道组成
要正确使用-fork 和-combine(-fork<id> 指明了需要执行的命令以及顺序 )
-combine只有在合并多个plugins输出的文件时才使用,作为接下来的plugin的出入
每一个fork都有一个id
Output from a Sub-Pipeline can be used as Input to a another Sub-Pipeline by referencing with the flag -input. (i.e. -input1)
Each Sub-Pipeline (i.e. -fork) runs in it’s own CPU Process (i.e. Thread)
run_pipeline.pl -fork1 <plugin> <plugin> -endPlugin -fork2 <plugin> <plugin> -endPlugin -fork3 <plugin> <plugin> <plugin>
run_pipeline.pl -fork1 <plugin> <plugin> -endPlugin -fork2 <plugin> -input1 <plugin> -endPlugin -fork3 <plugin> -input1 <plugin> <plugin>
run_pipeline.pl -fork1 <plugin> <plugin> -endPlugin -fork2 <plugin> <plugin> -endPlugin -combine3 -input1 -input2 <plugin> <plugin> <plugin>
run_pipeline.pl -fork1 <plugin> <plugin> -fork2 <pluginA> <pluginB> -input1
run_pipeline.pl -fork1 -importGuess mdp_genotype.hmp.txt -FilterSiteBuilderPlugin -siteMinAlleleFreq 0.01 -endPlugin -fork2 -importGuess mdp_phenotype.txt -excludeLastTrait -combine3 -input1 -input2 -intersect -FixedEffectLMPlugin -endPlugin -export glm_output
run_pipeline.pl -Xms512m -Xmx10g ...

我自己分析使用正常的代码

run_pipeline.pl -Xmx6G -importGuess zheng58_group_genotypegvcf_noother.vcf -ExportPlugin -saveAs zheng58_group.phy -format Phylip_Inter 
#第一次在运行这个命令是报错了,然后我将B73_V4_ctg、Pt和Mt这些开头的都去掉就没问题了
PhyML-3.1_linux64 -i zheng58_group.phy -d generic -b 1000 -m HKY85 -f m -v e -a e -o tlr

参考

Tassel 5.0 Pipeline (Command Line Interface)
Tassel 5 Pipeline Tutorial

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