convert CHR:POS to rsID

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Jul 17, 2024, 6:30:59 AM (3 days ago) Jul 17

to plink2-users

Hello, first I really appreciate your answer of my last question.

I realized that my approach was completely wrong.

Anyway,

I try to change POS to rsID at .bim file (ex. 1:759293_A/T -> rs10157329).

I already know about duplicate-ID problems, but I need this procedure for my process.

I used PLINK 2.0's --recover-var-ids command on the GRCh37 1000 Genomes phase 3 .pvar.zst file (my file based on GRCh37).

Here’s my log

PLINK v2.00a6 64-bit (4 Jul 2024)

Options in effect:

--bfile hexa

--make-bed

--out hexaa

--recover-var-ids all_phase3.pvar strict-bim-order partial force

Hostname: DESKTOP-K1N33HD

Working directory: c:\test

Start time: Wed Jul 17 16:40:16 2024

Random number seed: 1721202016

16145 MiB RAM detected; reserving 8072 MiB for main workspace.

Allocated 1914 MiB successfully, after larger attempt(s) failed.

Using up to 12 threads (change this with --threads).

58693 samples (0 females, 0 males, 58693 ambiguous; 58693 founders) loaded from

hexa.fam.

5418317 variants loaded from hexa.bim.

Note: No phenotype data present.

--recover-var-ids: 84805962 lines scanned.

--recover-var-ids: 3820254/5418317 IDs updated.

Writing hexaa.fam ... done.

Writing hexaa.bim ... done.

Writing hexaa.bed ... done.

End time: Wed Jul 17 16:47:10 2024

3820254 IDs updated but the rest is still in pos state.

From what I've found in this plink2 user conversation, I think there is a way for me to use --update-name command. I'm sorry to say this, but even after reading the explanation, I don't understand it at all.

To sum up,

1) If --recover-var-ids command is appropriate for my task, What more commands should I add?

2) If --update-name command is appropriate for my task, I would like to know details about the direction of progress.

I already download the SNP file from UCSC, and the file form is as follows.

585 chr1 10019 10020 rs775809821
585 chr1 10038 10039 rs978760828
585 chr1 10042 10043 rs1008829651
585 chr1 10050 10051 rs1052373574
585 chr1 10051 10051 rs1326880612

In --update-name <filename> [new ID col. number] [old ID col.] [skip] <-this explanation

In this situation, I didn't know what to add at [new ID col. number] [old ID col.], so I ran it without adding anything, and of course there was no change.

3) I would appreciate it if you could let me know if there is another way to access it other than the above commands.