Convert plink files from
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11 weeks 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!

plink convert bim rsIDs genetics • 309 views
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You may try posting on the Google Group: https://groups.google.com/g/plink2-users

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Thank you will do!

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