一、vcf文件格式转换

转换成plink格式

vcftools --vcf SNP_merge.vcf --plink --out SNP
plink --file SNP --make-bed --out SNP_b
plink --bfile SNP_b --freq --missing --within data.clust
gzip plink.frq.strat
python2 ../bin/gene_flow/plink2treemix.py plink.frq.strat.gz treemix.frq.gz

注意：plink2treemix.py从https://bitbucket.org/nygcresearch/treemix/wiki/Home下载，是用python2写的。

data.clust格式：

ind_10  ind_10  pop1
ind_11  ind_11  pop1
ind_12  ind_12  pop2
ind_13  ind_13  pop2
ind_14  ind_14  pop3

二、treemix使用

#! /bin/sh
treemix -i treemix.frq.gz -m 0 -g out_tree.vertices.gz out_tree.edges.gz -root  Bol  -bootstrap -k 1000 -noss -o  bra0
treemix -i treemix.frq.gz -m 1 -g out_tree.vertices.gz out_tree.edges.gz -root Bol  -bootstrap -k 1000 -noss -o  bra1
treemix -i treemix.frq.gz -m 2 -g out_tree.vertices.gz out_tree.edges.gz -root Bol  -bootstrap -k 1000 -noss -o  bra2
treemix -i treemix.frq.gz -m 3 -g out_tree.vertices.gz out_tree.edges.gz -root Bol  -bootstrap -k 1000 -noss -o  bra3
treemix -i treemix.frq.gz -m 4 -g out_tree.vertices.gz out_tree.edges.gz -root Bol  -bootstrap -k 1000 -noss -o  bra4
treemix -i treemix.frq.gz -m 5 -g out_tree.vertices.gz out_tree.edges.gz -root Bol  -bootstrap -k 1000 -noss -o  bra5
treemix -i treemix.frq.gz -m 6 -g out_tree.vertices.gz out_tree.edges.gz  -root Bol  -bootstrap -k 1000 -noss -o  bra6
treemix -i treemix.frq.gz -m 7 -g out_tree.vertices.gz out_tree.edges.gz   -root Bol  -bootstrap -k 1000 -noss -o  bra7
treemix -i treemix.frq.gz -m 8 -g out_tree.vertices.gz out_tree.edges.gz   -root Bol  -bootstrap -k 1000 -noss -o  bra8

参考：
https://bitbucket.org/nygcresearch/treemix/wiki/Home
https://zhuanlan.zhihu.com/p/109071456