统计文件某列各项或某项出现次数(VCF文件中每个染色体信息)
摘要：#!/bin/bash grep -v ^# $i|awk '{sum[$1+=1]END{for(i in sum)print i"\t" sum[i]}' >chr_info #按大小排序 sort -n chr_info #某列求和 awk '{sum +=$2;END {print sum}
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LDdecay按照染色体分开画
摘要：.: read.table("Fig_chr1_wild_africa.bin")->data1read.table("Fig_chr2_wild_africa.bin")->data2read.table("Fig_chr3_wild_africa.bin")->data3read.table("
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R语言数据处理60题
摘要：#author lee #date 2021.8.26 library(tidyverse) #1创建数据 df <- data.frame( "grammer" = c("Python","C","Java","GO",NA,"SQL","PHP","Python"), "score" = c(1
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shell 下实现VLOOKUP
摘要：#!/bin/bash #vlookup #author lee #date 2021.8.26 if [ $# -ne 2 ] then echo "File number supplied is not right" echo "Input File1 that have your info"
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plink-pca分析
摘要：#！/bin/bash plink --bfile ../cold/cold.filter --pca 2 --out 2pc https://zhuanlan.zhihu.com/p/357759550 向mrMLM包中添加主成分，需要加两行header
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群体结构分析admixture
摘要：#PBS -N admixture #PBS -l nodes=1:ppn=12 #PBS -q middle cd $PBS_O_WORKDIR for K in {1..15}; do ~/biosoft/dist/admixture_linux-1.3.0/admixture -j12 --c
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从ID到GWAS
摘要：#!/bin/bash #use id to keep vcf and hmp #author leee #time 2021.8.23 echo "Input ID_file as args1 and Phenofile as args2!" >>${1}.log echo "Your ID_fi
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mrMLM-qsub
摘要：注意表型首行使用标签<Trait> 脚本mrmlm.r #!/public/home/caisl/biosoft/miniconda3/envs/r4.1/bin/R library('mrMLM') mrMLM(fileGen='184.hmp.txt',filePhe='pheno',Genfo
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从基因到单倍型-水稻GWAS
摘要：单倍型分析 ###1.根据GWAS结果找到一系列基因 推荐使用rMVP,mrMLM等R语言包，速度快，直接出图 ###2. 对得到的结果利用snpEff或者annovar进行注释 注意选择对应的基因组文件（及染色体chr1/1) 为了搭配后面用的candihap软件，这里使用annovar进行注释
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