根据VCF构建进化树

VCF2Dis，是一款计算根据vcf文件计算距离矩阵的小工具

1 安装

下载后

tar -zxvf  VCF2DisXXX.tar.gz
cd VCF2DisXXX
make
# 添加环境变量即可

2 示例文件进行简单使用

Usage: VCF2Dis -i <in.vcf>  -o  <p_dis.mat>

          #1.0) Parameters can used as short letter
                  Such as : [-i] short for [-InPut], [-o] for [-OutPut],[-s] for [-SubPop], [-k] for [-KeepMF]

          #2.1) To new all the sample p_distance matrix based VCF, run VCF2Dis directly
                   ./bin/VCF2Dis    -i  in.vcf.gz  -o p_dis.mat

          #2.2) To new sub group sample p_distance matrix ; Put their sample name into File sample.list
                 ./bin/VCF2Dis  -InPut  chr1.vcf.gz chr2.vcf.gz  -OutPut p_dis.mat  -SubPop  sample.list

          #3.0) Default use all site to join the Calculation. To run the bootstrap tree , can run muti-time with using part of site, Para [-Rand]
                 ./bin/VCF2Dis  -InPut  in.vcf.gz  -OutPut p_dis.mat   -Rand  0.25

操作

# 对所有样本进行计算距离矩阵
../bin/VCF2Dis  -InPut  in.vcf.gz       -OutPut p_dis.mat

# 对部分样本计算
../bin/VCF2Dis  -InPut  in.vcf.gz       -OutPut p_dissub.mat  -SubPop  sample.list
# 其中
head sample.list
S010
S033
S186
S123
S124
S011

得到的结果如下所示

3 构建树

• 在线构建
  上传距离矩阵到在线网站, FastMe2.0。上传以后，选择Data type为Distance matrix。 然后点击最下方的execute & email results即可。邮箱也可不写。
  最终得到一个.nwk的文件，导入iTOl即可查看，如下所示
  

  image.png

• 也可通过phylip进行构建树
  具体可以查看# 序列比对和构建进化树（clustalw和phylip）

参考

• VCF2Dis