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Converting SNP from chr:pos to rs number using PLINK?

Hi,

I have a .txt file with multiple columns, one of which lists SNPs in chr:pos format. Is it possible to convert from chr:pos to rs number using PLINK? If so, what commands are required.

Thanks!

plink snp
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updated by Ram Ram • written by dam4l dam4l

Additionally, I have ~ 15 million SNPs.

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written by dam4l dam4l

Do you have a list with the corresponding rs? Ex: 1:123467932 rs123456789

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updated by Ram Ram • written by Maxime Lamontagne Maxime Lamontagne

No I don't. I just have the SNPs in a .bim file with the following columns:

1    1:693731    0    693731    G    A
1    1:706992    0    706992    T    C
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updated by Ram Ram • written by dam4l dam4l

To change the SNP name, you need a list with all SNPs available.

  1. Go to UCSC Table Browser and download a list of all available SNPs with chr, pos and rs number.
  2. Create a file with chr:pos in column 1 and rs number in column 2.
  3. In PLINK, use options --update-map and --update-name to change your SNPs name. WARNING: Some position have more than one SNP.
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updated by Ram Ram • written by Maxime Lamontagne Maxime Lamontagne

Thanks for your reply! Which settings on the UCSC Table Browser will allow me to download this list?

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updated by Ram Ram • written by dam4l dam4l
  • clade: Mammal
  • genome: Human
  • assembly: Same as your SNPs
  • group: Variation
  • track: All SNPs (latest)
  • table: All SNPs
  • region: Genome
  • output format: selected fields from primary and related tables
  • output file: All-SNPs.txt
  • file type returned: plain text

get output

Select Fields from...

  • chrom
  • chromEnd
  • name
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updated by Ram Ram • written by Maxime Lamontagne Maxime Lamontagne

Thanks so much!

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written by dam4l dam4l

Thank you so much! I followed your way to download the Chromosome/position/rs# information, and ready to do the convertion using plink --update-name flag , but realized that there are some positions with multiple rs# and plink just stoped with error. How can I delete duplication from the >100000000 SNPs (I did a whole genome imputation so downloaded SNPs of whole genome as you suggested)?

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updated by Ram Ram • written by chenchunhuichina • chenchunhuichina

You have two possible solution.

  1. Do not update any SNP with two or more possible rs. It's not perfect, but it's a good temporary solution.
  2. Find the good rs by comparing alleles. On UCSC, you can download alleles for each snp. Then choose the right rs.
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updated by Ram Ram • written by Maxime Lamontagne Maxime Lamontagne

Hi,

I'm kind of facing similar error of duplicate variant ID after using --update-name flag in plink. My error is shown below. 

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

When you are saying for the possible solution of 1) Do not update any SNP with two ore more possible rs. What do you mean by that? How can I do not update the duplicate chr:position rs ID?

Thank you for your help!

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updated by Ram Ram • written by jystat • jystat

re: "2." How do you download the alleles for each SNP from UCSC? and how do you choose the correct rsid from comparing alleles?

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written by hi.there • hi.there

Hi all! I don't know if this is a more recent thing, but I was not able to download the file using the method described here, because the download times out as the file is too big for the table browser. I found the file containing all SNPs in the UCSC directory ( http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/snp151.txt.gz ).

[UPDATE] But actually, I used only the common SNPs table.

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written by rodd rodd

Thanks a lot! I have a question. Does "position" in "CHR:POSITION" SNP IDs refer to chromosome start or end position?

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written by bigfoot • bigfoot

I think it's end, but double check it on UCSC browser by viewing your SNP of interest. But bear in mind that this rule only works for single nucleotide variants (multiallelic variants do not obey this rule).

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written by rodd rodd

where to put the file with chr:pos and rsid?

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written by heqianchange • heqianchange

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