使用hiblup计算个体杂合率和个体纯合率

 

001、计算纯合率

(base) [root@PC1 test]# ls
outcome.bed  outcome.fam  outcome.map    outcome.ped
outcome.bim  outcome.log  outcome.nosex
(base) [root@PC1 test]#
(base) [root@PC1 test]# hiblup --bfile outcome --homo --out test &> /dev/null
(base) [root@PC1 test]# ls                        ## 计算个体纯合率
outcome.bed  outcome.fam  outcome.map    outcome.ped  test.log
outcome.bim  outcome.log  outcome.nosex  test.homo
(base) [root@PC1 test]# cat test.homo     ## 结果
id      a1a1    a2a2
1       0.4     0.4
2       0.2     0.6
3       0       1
4       0       1
5       0       1
6       0       1
(base) [root@PC1 test]# cat outcome.ped
DOR     1       0       0       0       -9      T T     C C     A A     G G     A G
DOR     2       0       0       0       -9      T T     G C     G G     G G     G G
DOR     3       0       0       0       -9      G G     C C     G G     G G     G G
DOR     4       0       0       0       -9      G G     C C     G G     G G     G G
DOR     5       0       0       0       -9      G G     C C     G G     G G     G G
DOR     6       0       0       0       -9      G G     C C     G G     G G     G G

 

002、计算杂合率

(base) [root@PC1 test]# ls
outcome.bed  outcome.fam  outcome.map    outcome.ped
outcome.bim  outcome.log  outcome.nosex
(base) [root@PC1 test]# hiblup --bfile outcome --hete --out test &> /dev/null
(base) [root@PC1 test]# ls                   ## 计算个体杂合率
outcome.bed  outcome.fam  outcome.map    outcome.ped  test.log
outcome.bim  outcome.log  outcome.nosex  test.hete
(base) [root@PC1 test]# cat test.hete        ## 计算结果
id      a1a2
1       0.2
2       0.2
3       0
4       0
5       0
6       0
(base) [root@PC1 test]# cat outcome.ped
DOR     1       0       0       0       -9      T T     C C     A A     G G     A G
DOR     2       0       0       0       -9      T T     G C     G G     G G     G G
DOR     3       0       0       0       -9      G G     C C     G G     G G     G G
DOR     4       0       0       0       -9      G G     C C     G G     G G     G G
DOR     5       0       0       0       -9      G G     C C     G G     G G     G G
DOR     6       0       0       0       -9      G G     C C     G G     G G     G G