混池测序计算序列段Tajmas'D

1.用Bam生成mpileup文件

#!bash
cat filename.txt while read line  #bam文件地址名在filename.txt里
do
  ref=/home/fanbaitong/inut/Yunnan15nation/GRCH37/human_g1k_v37_decoy.fa
  prefix=$(basename $line) 
        samtools mpileup -q 5 -d 180 -Q 5 -C 50 -f $ref $line  > $prefix.mpileup
done

2.用mpileup文件计算序列片段的被选择情况Tajmas'D

nohup perl  /home/fanbaitong/software/popoolation_1.2.2/Variance-sliding.pl  --input AChun.mpileup --output AChun.tajmasd --measure D --window-size 100000 --step-size 100000 --min-count 2 --min-coverage 5 --max-coverage 220 --min-qual 5 --pool-size 92  --min-covered-fraction 0.5  --measure  D  --fastq-type  illumina &  #防止稀有突变丢失，质量值设置为5

于是就得到了10KB为单位的人群基因组Tajmas‘D值
软件下载地址：
popoolation download | SourceForge.net
软件用法：
popoolation / Wiki / Manual (sourceforge.net)

参考文章：

Article Source: [**PoPoolation: A Toolbox for Population Genetic Analysis of Next Generation Sequencing Data from Pooled Individuals**](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0015925 "Back to original article")
Kofler R, Orozco-terWengel P, De Maio N, Pandey RV, Nolte V, et al. (2011) PoPoolation: A Toolbox for Population Genetic Analysis of Next Generation Sequencing Data from Pooled Individuals. PLOS ONE 6(1): e15925. [https://doi.org/10.1371/journal.pone.0015925](https://doi.org/10.1371/journal.pone.0015925)

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中国医学科学院
医学生物学研究所
遗传学 范同学
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