plink软件中--set-missing-var-ids @:#的作用

1、测试数据

[root@linuxprobe test]# ls
test.map  test.ped
[root@linuxprobe test]# cat test.map  ## 测试数据snpID为.
1       .       0       55910
1       .       0       85204
1       .       0       122948
1       .       0       203750
1       .       0       312707
1       .       0       356863
1       .       0       400518
1       .       0       487423
[root@linuxprobe test]# cat test.ped
DOR     1       0       0       0       -9      G A     G G     G G     G C     G G     C C     C C     G G
DOR     2       0       0       0       -9      A A     G G     A G     C C     G G     G C     C C     G G
DOR     3       0       0       0       -9      A A     G G     A G     G C     C G     C C     G G     G G
DOR     4       0       0       0       -9      A A     G G     G G     G G     C G     G G     G G     G G
DOR     5       0       0       0       -9      A A     G G     A G     G C     G G     C C     G G     G G
DOR     6       0       0       0       -9      A A     G G     A A     C C     G G     C C     G G     G G
DOR     7       0       0       0       -9      G G     G G     G G     C C     G G     C C     G G     A G
DOR     9       0       0       0       -9      G G     G G     G G     C C     G G     C C     G G     A G

 

2、

 plink --file test --set-missing-var-ids @:# --recode tab --out a ;rm *.log *.nosex
[root@linuxprobe test]# cat a.map  ## 可见snpID发生变化
1       1:55910 0       55910
1       1:85204 0       85204
1       1:122948        0       122948
1       1:203750        0       203750
1       1:312707        0       312707
1       1:356863        0       356863
1       1:400518        0       400518
1       1:487423        0       487423
[root@linuxprobe test]# md5sum *.ped
09e293ef08104b377871b606816f52a6  a.ped
09e293ef08104b377871b606816f52a6  test.ped

 

 plink --file test --set-missing-var-ids @:#\$1,\$2 --recode tab --out a; rm *.log *.nosex  
[root@linuxprobe test]# cat a.map  ## 加上了snp组合
1       1:55910A,G      0       55910
1       1:852040,G      0       85204
1       1:122948A,G     0       122948
1       1:203750C,G     0       203750
1       1:312707C,G     0       312707
1       1:356863C,G     0       356863
1       1:400518C,G     0       400518
1       1:487423A,G     0       487423
[root@linuxprobe test]# md5sum *.ped
09e293ef08104b377871b606816f52a6  a.ped
09e293ef08104b377871b606816f52a6  test.ped
[root@linuxprobe test]# cat a.ped
DOR     1       0       0       0       -9      G A     G G     G G     G C     G G     C C     C C     G G
DOR     2       0       0       0       -9      A A     G G     A G     C C     G G     G C     C C     G G
DOR     3       0       0       0       -9      A A     G G     A G     G C     C G     C C     G G     G G
DOR     4       0       0       0       -9      A A     G G     G G     G G     C G     G G     G G     G G
DOR     5       0       0       0       -9      A A     G G     A G     G C     G G     C C     G G     G G
DOR     6       0       0       0       -9      A A     G G     A A     C C     G G     C C     G G     G G
DOR     7       0       0       0       -9      G G     G G     G G     C C     G G     C C     G G     A G
DOR     9       0       0       0       -9      G G     G G     G G     C C     G G     C C     G G     A G

 

plink --file test --set-missing-var-ids @:#[b37]\$1,\$2 --recode tab --out a; rm *.log *.nose
[root@linuxprobe test]# md5sum *.ped
09e293ef08104b377871b606816f52a6  a.ped
09e293ef08104b377871b606816f52a6  test.ped
[root@linuxprobe test]# cat a.map ## 同上 ？？
1       1:55910[b37]A,G 0       55910
1       1:85204[b37]0,G 0       85204
1       1:122948[b37]A,G        0       122948
1       1:203750[b37]C,G        0       203750
1       1:312707[b37]C,G        0       312707
1       1:356863[b37]C,G        0       356863
1       1:400518[b37]C,G        0       400518
1       1:487423[b37]A,G        0       487423