Plink update name flag, setting column names
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12 days ago
salman_96 ▴ 20

Hi I am trying to convert snp coordinates to rsIDs by using the flag --update-name

I am not sure if I am using it correctly my command is

plink1.9 --bfile files --update-name snps_coordinates_rs_IDs [1] [2] --out Test_update_name

I am using [1] [2] to dedicate columns. The snp_coordinate file looks like this . The first column has coordinates the second has rsIDs

1:48899:G:A rs974664996

1:114531:G:C rs918310516

1:133360:T:C rs974682326

1:541281:GGGCCAACCACAGGACA:G rs752188509

1:564782:T:C rs879089824

1:636747:C:T rs974667799

My .bim file has coordinates which I want to convert to rsIDs. I am getting this output Error: Invalid --update-name column number.

Am I missing column names PLease assist

Plink1.9 --update-name • 252 views
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Entering edit mode
12 days ago
  1. Remove the square brackets from your command line. See the "Interpreting our flag usage summaries" section under https://www.cog-genomics.org/plink/1.9/general_usage .
  2. Swap the order of the two numbers: "2 1" instead of "1 2". The --update-name usage summary is "--update-name <filename> [new ID col. number] [old ID col.] [skip]"; the new-ID column number comes BEFORE the old-ID column number. Or you could just remove the column numbers entirely, since "2 1" corresponds to the default behavior (this is mentioned in the first paragraph of the --update-name documentation).
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Hi I have done that but my .bim file has coordinates instead of rsIDs I was expecting rsIDs

The snp_coorinates file look like this

rs2281304 1:6147134:C:A,G,T

rs11584419 1:6147341:A:C

rs2273043 1:6149053:C:T

rs2273042 1:6149122:G:A

The files.bim file looks like this

1 1:851390:G:T 0 851390 T G

1 1:852758:G:C 0 852758 C G

1 1:853239:A:G 0 853239 G A

The generated .bim file is also similar to previous .bim file, I was expecting rs IDs but looks like this

1 1:730087:T:C 0 730087 C T

1 1:752721:A:G 0 752721 A G

1 1:754105:C:T 0 754105 T C

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Please reread the second half of my answer.

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Hi when I do not add 1 and 2 in the plink command I get results but the bim in results have same coordinates instead I was expecting rsIDs. I have edited my previous comment too (the rsIDs and coordinate file has columns inverted now)

When I use --update-name 2 1 I get error Failed to open 2 when I use --update-name 1 2 it says Failed to open 1

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Why did you remove the filename from your --update-name command?

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10 days ago
salman_96 ▴ 20

Hi, I was able to solve this issue Thank you for help.

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