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2.5 years ago
ravibot
▴
10
I have plink files where the .bim file is in the following format, and I want to convert the chr:pos column into rsIDs.
1 1:10177:A:AC 0 10177 AC A
1 1:10352:T:TA 0 10352 TA T
1 1:11008:C:G 0 11008 G C
1 1:11012:C:G 0 11012 G C
1 1:13116:T:G 0 13116 G T
1 1:13118:A:G 0 13118 G A
1 1:13273:G:C 0 13273 C G
1 1:14464:A:T 0 14464 T A
1 1:14599:T:A 0 14599 A T
1 1:14604:A:G 0 14604 G A
1 1:14930:A:G 0 14930 G A
1 1:15211:T:G 0 15211 T G
1 1:15274:A:G 0 15274 G A
1 1:15274:A:T 0 15274 A T
1 1:15820:G:T 0 15820 T G
1 1:15903:G:GC 0 15903 GC G
1 1:18849:C:G 0 18849 C G
1 1:30923:G:T 0 30923 G T
1 1:49298:T:C 0 49298 T C
1 1:49554:A:G 0 49554 G A
1 1:51479:T:A 0 51479 A T
1 1:52238:T:G 0 52238 T G
1 1:54490:G:A 0 54490 A G
I also have the following file downloaded from the UCSC consisting of all the SNPs (goes all the way through chr22).
#chrom chromEnd name
chr1 100663297 rs1235665665
chr1 1048577 rs1346354302
chr1 62914560 rs538775156
chr1 196083715 rs1467218511
chr1 224395264 rs1488102548
chr1 246415379 rs1177496554
chr1 248512513 rs1485351626
chr1 1966085 rs1434739345
chr1 20316161 rs1364715928
chr1 22151182 rs1479725788
chr1 22282249 rs1334705775
chr1 24641536 rs1224526302
chr1 27918338 rs1286521817
chr1 36962304 rs1245424846
chr1 38928394 rs1455081642
chr1 40370176 rs564192510
chr1 49807374 rs1474027475
chr1 54263809 rs1273015241
chr1 54263814 rs1300134828
chr1 54263808 rs1330645881
chr1 55181315 rs1419499904
chr1 61341699 rs146746778
chr1 61341703 rs1337374129
chr1 64880661 rs1285464921
chr1 68026376 rs1361777872
I understand that the --update-name
flag in plink is supposed to be the way to change these, but I keep getting an error has fewer tokens than expected
.
Can anyone please help me to get this to work?
Thanks!
You may try posting on the Google Group: https://groups.google.com/g/plink2-users
Thank you will do!