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