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）
