======简介======
FST​，全称为fixation index，是一种用于衡量群体间分化程度的统计检验量（由Wright’s F-statistics衍生而来）。 一般从SNP或microsatellites数据计算得到，且一般用在群体遗传学分析中.
核苷酸多态性（Pi）是衡量特定群体多态性高低的参数，是指在同一群体中随机挑选的两条DNA序列在各个核首酸位点上核昔酸差异的均值。核苷酸多态性（Pi）能揭示不同物种核酸序列的变异大小，变异度较高的区域可以为种群遗传学提供潜在的分子标记。
======功能======
检测基因组选择信号分析
======数据准备======
单个样本的vcf文件
群call的vcf

======数据分析======
1 示例路径======
/TJPROJ6/AFS_RESEQ/Proj/hongxiang/05.AFS/FST_Pi_window
======
2 分析脚本
<code>
/PUBLIC/software/RESEQ/software/vcftools_v0.1.15/setup/bin/vcftools --gzvcf ./all.vcf.gz --keep ./yuan.list --recode --recode-INFO-all --out ./01.Pi/test/yuan
/PUBLIC/software/RESEQ/software/vcftools_v0.1.15/setup/bin/vcftools --vcf ./01.Pi/test/yuan.recode.vcf --window-pi 2000 --window-pi-step 1000 --out ./01.Pi/test/yuan
#export PYbarthiiONPAbarthii=""
export PYTHONPATH=""
/TJPROJ6/AFS_RESEQ/Proj/liangjifeng/software/miniconda3/envs/python3.5/bin/python /TJNAS01/AFS_RESEQ/Share/GWAS/PopEvolution_pip/Config/shell_bin/06.select_sweep/00.bin/sort_plot_pos.py -d ./01.Pi/test/yuan.windowed.pi -o ./01.Pi/test/yuan.windowed.pi.tem -fai ./genome.fa.fai -chr ./chr.list -head True
awk '{print $1"\t"$2"\t"$5"\t"$NF}' ./01.Pi/test/yuan.windowed.pi.tem > ./01.Pi/test/yuan.windowed.pi.plot


</code>


<code>
/PUBLIC/software/RESEQ/software/vcftools_v0.1.15/setup/bin/vcftools --gzvcf ./all.vcf.gz --weir-fst-pop ./wild.list --weir-fst-pop ./japonica.list --fst-window-size 2000 --fst-window-step 1000 --out ./wild_japonica
/PUBLIC/software/public/System/Perl-5.18.2/bin/perl /TJNAS01/AFS_RESEQ/Share/GWAS/PopEvolution_pip/Config/shell_bin/06.select_sweep/00.bin/Fst_plot.pl -f ./wild_japonica.windowed.weir.fst -fai ./genome.fa.fai -chr ./chr.list -o ./wild_japonica.all.fst -sample wild_japonica -top 0.05 -win 1bp

</code>
<code>
library(ggplot2)

data<-read.table("all.fst",header=T,sep="\t")

pdf("new_fst.pdf",width=15,height=4)
head(data)
#data1<-filter(data,CHROM!="YY")
data$CHROM<-factor(data$CHROM,)
#p <- ggplot(data,aes(x=BIN_START/1000000,y=PI,color=sample))+ facet_wrap(data$sample,ncol=1)+ geom_line(size=0.5) + xlab("Chr.1(Mp)")+ ylab("Nucleotide diversity(Pi)")
p <- ggplot(data,aes(x=BIN_START,y=MEAN_FST,color=group))+ geom_line(size=0.5) + xlab("Chr.1(bp)")+ ylab("Mean Fst") +scale_x_continuous(breaks=seq(14438000,14462000,2000)) 
#+ scale_y_continuous(breaks=seq(0,0.04,0.01))
#p <- ggplot(data,aes(x=CHROM,y=TajimaD,color=CHROM)) + geom_line(size=0.5) + xlab("Chromosome1 (Mb)")+ ylab("TajimaD")

p + theme_bw(base_size =15) + theme(plot.margin = margin(t = 1, r = 1, b = 2, l = 1, unit = "cm"))

dev.off()

</code>
======交付结果======
pi和FST相关表格和图片