VCF2Dis，是一款計算根據vcf檔案計算距離矩陣的小工具

1 安裝

下載後

tar -zxvf  VCF2DisXXX.tar.gz
cd VCF2DisXXX
make
# 新增環境變數即可

2 示例檔案進行簡單使用

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

# 對所有樣本進行計算距離矩陣
../bin/VCF2Dis  -InPut  in.vcf.gz       -OutPut p_dis.mat

# 對部分樣本計算
../bin/VCF2Dis  -InPut  in.vcf.gz       -OutPut p_dissub.mat  -SubPop  sample.list
# 其中
head sample.list
S010
S033
S186
S123
S124
S011

得到的結果如下所示

3 構建樹

• 線上構建
  上傳距離矩陣到線上網站, FastMe2.0。上傳以後，選擇Data type為Distance matrix。 然後點選最下方的execute & email results即可。郵箱也可不寫。
  最終得到一個.nwk的檔案，匯入iTOl即可檢視，如下所示
  

• 也可通過phylip進行構建樹
  具體可以檢視# 序列比對和構建進化樹（clustalw和phylip）

參考

• VCF2Dis