使用pixy计算群体遗传学统计量

1 数据过滤

过滤参数：过滤掉次等位基因频率（minor allele frequency，MAF）低于0.05、哈达-温伯格平衡（Hardy– Weinberg equilibrium，HWE）对应的P值低于1e-10或杂合率（heterozygosity rates）偏差过大（± 3 SD）的位点：
去除杂合率（heterozygosity rates）偏差过大（± 3 SD）的个体：
假设，基于Plink计算结果，需要移除sample1（高杂合或低杂合）:

#vcftools version:
nohup vcftools --vcf snps_filtered.vcf --remove-indels --maf 0.05 --hwe 1e-10 --max-missing 0.8 --min-meanDP 20 --max-meanDP 500 --remove-indv sample1 --recode --stdout > snps_maf0_05_hwe1e-10_missing0_8.vcf &

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vcftools生成的文件中会包含命令行输出，使用sed移除：

nohup sed -i '1,30d' snps_maf0_05_hwe1e-10_missing0_8.vcf &
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压缩：

bgzip snps_maf0_05_hwe1e-10_missing0_8.vcf
tabix snps_maf0_05_hwe1e-10_missing0_8.vcf.gz
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2 计算$F_{ST}、D_{XY}、Pi$

安装软件包

nohup pixy --stats pi fst dxy --vcf snps_maf0_05_hwe1e-10_missing0_8.vcf.gz --populations pop.txt --window_size 10000 --bypass_invariant_check 'yes' --n_cores 15 --output_folder results &

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3 可视化

可视化之前需要将染色体编号替换为数值：

bash ~/gaoyue/GWAs/script/chr_tran.sh raw_results/pixy_dxy.txt results/pixy_dxy.txt
bash ~/gaoyue/GWAs/script/chr_tran.sh raw_results/pixy_fst.txt results/pixy_fst.txt
bash ~/gaoyue/GWAs/script/chr_tran.sh raw_results/pixy_pi.txt results/pixy_pi.txt
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#load packages:
library(ggplot2)
library(tidyverse)

#---------------------------------------------------------------------------------#
#             1.define a function to convert the pixy outputs                     #
#---------------------------------------------------------------------------------#
pixy_to_long <- function(pixy_files){

  pixy_df <- list()

  for(i in 1:length(pixy_files)){

    stat_file_type <- gsub(".*_|.txt", "", pixy_files[i])

    if(stat_file_type == "pi"){

      df <- read_delim(pixy_files[i], delim = "\t")
      df <- df %>%
        gather(-pop, -window_pos_1, -window_pos_2, -chromosome,
               key = "statistic", value = "value") %>%
        rename(pop1 = pop) %>%
        mutate(pop2 = NA)

      pixy_df[[i]] <- df


    } else{

      df <- read_delim(pixy_files[i], delim = "\t")
      df <- df %>%
        gather(-pop1, -pop2, -window_pos_1, -window_pos_2, -chromosome,
               key = "statistic", value = "value")
      pixy_df[[i]] <- df

    }

  }

  bind_rows(pixy_df) %>%
    arrange(pop1, pop2, chromosome, window_pos_1, statistic)

}

#---------------------------------------------------------------------------------#
#                      2.use new function we just defined:                        #
#---------------------------------------------------------------------------------#
## Rcau则替换为对应的文件夹
pixy_folder <- "/nfs_fs/nfs3/gaoyue/gaoyue/Fst/Rdeb_Fst/results/"
pixy_files <- list.files(pixy_folder, full.names = TRUE)
pixy_df <- pixy_to_long(pixy_files)

#---------------------------------------------------------------------------------#
#                                      3.plot:                                    #
#---------------------------------------------------------------------------------#
# create a custom labeller for special characters in pi/dxy/fst
pixy_labeller <- as_labeller(c(avg_pi = "pi",
                             avg_dxy = "D[XY]",
                             avg_wc_fst = "F[ST]"),
                             default = label_parsed)

# plotting summary statistics across all chromosomes
pixy_df %>%
  mutate(chrom_color_group = case_when(as.numeric(chromosome) %% 2 != 0 ~ "even",
                                 chromosome == "X" ~ "even",
                                 TRUE ~ "odd" )) %>%
  mutate(chromosome = factor(chromosome, levels = c(1:22, "X", "Y"))) %>%
  filter(statistic %in% c("avg_pi", "avg_dxy", "avg_wc_fst")) %>%
  ggplot(aes(x = (window_pos_1 + window_pos_2)/2, y = value, color = chrom_color_group))+
  geom_point(size = 0.5, alpha = 0.5, stroke = 0)+
  facet_grid(statistic ~ chromosome,
             scales = "free_y", switch = "x", space = "free_x",
             labeller = labeller(statistic = pixy_labeller,
                                 value = label_value))+
  xlab("Chromsome")+
  ylab("Statistic Value")+
  scale_color_manual(values = c("grey50", "black"))+
  theme_classic()+
  theme(axis.text.x = element_blank(),
        axis.ticks.x = element_blank(),
        panel.spacing = unit(0.1, "cm"),
        strip.background = element_blank(),
        strip.placement = "outside",
        legend.position ="none")+
  scale_x_continuous(expand = c(0, 0)) +
  scale_y_continuous(expand = c(0, 0), limits = c(0,NA))
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Ending!