1、测试数据
[root@linuxprobe test]# ls
outcome.map outcome.ped
[root@linuxprobe test]# cat outcome.ped
DOR 1 0 0 0 -9 C C C C A A G G A G G G G G G C
DOR 2 0 0 0 -9 C C G C A G G G G G A A A G C C
DOR 3 0 0 0 -9 G G C C A G G G G G G A A G G C
DOR 4 0 0 0 -9 G G C C G G G G G G A A G G G G
DOR 5 0 0 0 -9 G G C C G G G G G G A A A G G C
DOR 6 0 0 0 -9 G G C C G G G G G G A A A A C C
DOR 7 0 0 0 -9 G G C C G G A G A A A A G G C C
DOR 9 0 0 0 -9 G G C C G G A G A A A A G G C C
[root@linuxprobe test]# cat outcome.map
1 snp1 0 55910
1 snp2 0 85204
1 snp3 0 122948
1 snp4 0 203750
1 snp5 0 312707
1 snp6 0 356863
1 snp7 0 400518
1 snp8 0 487423
2、计算观测杂合度和期待杂合度
[root@linuxprobe test]# plink --file outcome --hardy --out test;rm *.nosex ## 加--hardy选项即可计算
[root@linuxprobe test]# cat test.hwe
CHR SNP TEST A1 A2 GENO O(HET) E(HET) P
1 snp1 ALL(NP) C G 2/0/6 0 0.375 0.01538
1 snp2 ALL(NP) G C 0/1/7 0.125 0.1172 1
1 snp3 ALL(NP) A G 1/2/5 0.25 0.375 0.3846
1 snp4 ALL(NP) A G 0/2/6 0.25 0.2188 1
1 snp5 ALL(NP) A G 2/1/5 0.125 0.4297 0.07692
1 snp6 ALL(NP) G A 1/1/6 0.125 0.3047 0.2
1 snp7 ALL(NP) A G 1/3/4 0.375 0.4297 1
1 snp8 ALL(NP) G C 1/3/4 0.375 0.4297 1
