update chr: position to rs ID

[Jongyun Jung]

Hi,

I'm trying to update my imputed data of chr:position to rs ID number. 

I found there is a similar solution in biostar as shown in the website below. 

https://www.biostars.org/p/171557/

For example, my .map file is looks like this:

1       1:748878        0       748878

1       1:751756        0       751756

1       1:752566        0       752566

1       1:752721        0       752721

1       1:752894        0       752894

1       1:753405        0       753405

And I downloaded my reference of rs ID file from (https://genome.ucsc.edu/cgi-bin/hgTables) as the file name is All-SNPs.txt. 

This file is looks like this:

#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

I run this command in my computer:

 plink --bfile HIPFXchr1 --update-map All-SNPs.txt --make-bed --out HIPFXchr1-updated

And then I got this error message of 

Ambiguous sex IDs written to HIPFXchr1-updated.nosex .

Error: Line 195333666 of --update-map file has fewer tokens than expected.

Could you help on this how can I change chr:position to rs ID? 

Thank you for your help!

[Christopher Chang]

1. You need to specify that variant IDs should be read from column 3, not column 1.  "--update-map All-SNPs.txt 2 3"

2. You may also need to remove the last line(s) of All-SNPs.txt if they don't adhere to the same format as the rest of the lines.  "head -n 195333665 All-SNPs.txt > truncated.txt"

[Jongyun Jung]

Hi Chris,

Thank you for your help.

After I truncated my All-SNPs.txt to  "head -n 195333665 All-SNPs.txt > All-SNPs-updated.txt", I was able to create new plink binary files with below command. 

plink --bfile HIPFXchr1 --update-map All-SNPs-updated.txt 2 3 --make-bed --out HIPFXchr1-updated

However, when I check the output of .bim file for rs ID number, it is still showing as chr:position number. 

 less -S HIPFXchr1-updated.bim

1       1:748878        0       748878  T       G

1       1:751756        0       751756  T       C

1       1:752566        0       752566  A       G

1       1:752721        0       752721  G       A

1       1:752894        0       752894  C       T

1       1:753405        0       753405  A       C

Could you help on this?

Thank you.

[Christopher Chang]

Oh, that's because --update-map isn't the command you wanted in the first place.  You want to run --update-name instead, after postprocessing the truncated All-SNPs.txt file to contain both the chr:pos and the new rsIDs.

[Jongyun Jung]

I tried with --update-name, but it is still showing chr:position in the updated .bim file. 

When I truncate my All-SNPs.txt file, should I have to extract only chr:pos and the new rsIDs?

Is it because my All-SNPs-updated.txt not format as chr:position?

Here is the head of All-SNPs-updated.txt. 

chr1    100663297       rs1235665665

chr1    1048577 rs1346354302

chr1    62914560        rs538775156

chr1    196083715       rs1467218511

chr1    224395264       rs1488102548

chr1    246415379       rs1177496554

chr1    248512513       rs1485351626

chr1    1966085 rs1434739345

Thank you.

[Christopher Chang]

Yes, it is because you did not reformat your All-SNPs-updated.txt to contain a chr:pos column.  Please reread my previous post.

[Jongyun Jung]

Hi Christopher,

I converted to the same format of chr:position for the .txt file as shown below. 

less -S All-SNPs-updated3.txt

1:100000002 rs1462733795

1:100000004 rs373074226

1:100000012 rs10875231

1:10000002 rs1323965099

1:100000048 rs898988451

1:100000049 rs1419136389

1:100000050 rs1410081010

1:100000056 rs575744361

1:10000005 rs1478843528

1:100000067 rs772996438

And when I run this command, 

 plink --bfile HIPFXchr1 --update-name All-SNPs-updated3.txt --make-bed --out HIPFXchr1-updated

I have error message of duplicate variant ID. 

PLINK v1.90b4.1 64-bit (30 Mar 2017)           www.cog-genomics.org/plink/1.9/

(C) 2005-2017 Shaun Purcell, Christopher Chang   GNU General Public License v3

Logging to HIPFXchr1-updated.log.

Options in effect:

  --bfile HIPFXchr1

  --make-bed

  --out HIPFXchr1-updated

  --update-name All-SNPs-updated3.txt

1031771 MB RAM detected; reserving 515885 MB for main workspace.

1874897 variants loaded from .bim file.

847 people (0 males, 0 females, 847 ambiguous) loaded from .fam.

Ambiguous sex IDs written to HIPFXchr1-updated.nosex .

Error: Duplicate variant ID '1:100002443' in --update-name file.

Is there any way that I can remove the duplicate variant ID in plink?

Thank you.

[Christopher Chang]

If you want to remove all duplicated IDs,

  plink --bfile HIPFXchr1 --write-snplist

  uniq -d plink.snplist duplicated.snplist

  plink --bfile HIPFXchr1 --exclude duplicated.snplist --out ...

should get the job done.

[Hannah Mandle]

Hi,

I have followed the same instructions in this thread to rename pos to rsID and it has worked for a subset of my files. However, some are stopping due to the error below:

 ./plink --bfile abi2_aac --update-map abi2b.txt  --recode A --out abi2_aa_rs
PLINK v1.90b7 64-bit (16 Jan 2023)             www.cog-genomics.org/plink/1.9/
(C) 2005-2023 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to abi2_aa_rs.log.
Options in effect:
  --bfile abi2_aac
  --out abi2_aa_rs
  --recode A
  --update-map abi2b.txt

15883 MB RAM detected; reserving 7941 MB for main workspace.
1727 variants loaded from .bim file.
2257 people (0 males, 0 females, 2257 ambiguous) loaded from .fam.
Ambiguous sex IDs written to abi2_aa_rs.nosex .
Error: Invalid bp coordinate on line 2 of --update-map file.

The .txt file looks like this: 

2:204183120 rs934711772
2:204183122 rs539421053
2:204183124 rs917373398
2:204183125 rs948908696
2:204183128 rs1044995944
2:204183129 rs888678182
2:204183139 rs1005785433
2:204183146 rs1471716359
2:204183154 rs1037297815
2:204183155 rs1261544649
....

If I delete the SNP at line 2, I then get an error at line 12, 21, etc. I have 208 genes I have filtered and need to rename to rsIDs and I am wondering if there is an easier workaround to this problem.

Thanks!

Hannah

[Hannah Mandle]

Nevermind! Solved using plink2