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PLINK .bim file shows chromosome 0 on Affymetrix chip

Currently I am working on PLINK genotype files. In the SNP file (.bim) the first two SNPs are showing as chromosome zero. The data has been genotyped on an Affymetrix Axiom array:

0       AFFX-SNP-000541 0       0       0       0
0       AFFX-SNP-002255 0       0       0       0

I am wondering why these first SNPs are coded as chromosome zero and how to deal with this. Should these just be excluded from further analysis?

Thank you

plink snp affymetrix
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updated by Ram Ram • written by philipovic • philipovic

Control SNPs? SNPs remove from current reference build?

Before removing them, look in old version of this chip. Maybe you could find why the were removed.

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updated by Ram Ram • written by Maxime Lamontagne Maxime Lamontagne

Did you able to find out answer for this?

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updated by Ram Ram • written by always_learning always_learning

3 answers

Did you able to find out answer for this ?, I have the same problem

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written by mariaf.betancur • mariaf.betancur

You can exclude them safely for further analysis.

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written by always_learning always_learning

But I have 23000 markers and 12909 markers are from zero chromosome? I dont know :/

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written by mariaf.betancur • mariaf.betancur

This might be because of that some arrays were designed long ago and some of these positions are discontinued or not available now.

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written by always_learning always_learning

I have the same problem with plink. But I cannot delete them in the .map file since the data will not be comparable anymore with .ped file. There are 1000 SNPs from Chr 0. How can I exclude them without having any problem with .ped file? Is there another way to proceed?

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written by Leonida Monaco • Leonida Monaco

Yeah, I tried it but I do not need to exclude a file, but the Chr 0 SNPs present in the .bim . When I use --exclude it says " No chr 0 file exists". I tried and succeeded in fixing X Y XY with 23 24 25 in the .map , but it's quite different. I am new of plink, only 2 months. Can you tell me something?

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written by Leonida Monaco • Leonida Monaco

The --exclude parameter expects a file with SNPs IDs that you want to exclude.

If you are sure that all those that have chromosome 0 are control probes, then remove them like this:

plink ... --not-chr 0

See here: https://www.cog-genomics.org/plink/1.9/order

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written by Kevin Blighe Kevin Blighe

Oh thank you man. It worked. At least there is no error warning now. I will check later the results, but plink is running. Have a great day

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written by Leonida Monaco • Leonida Monaco

Good day to you too, Sir / Madam.

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written by Kevin Blighe Kevin Blighe

These are control Affymetrix IDs. Control Affymetrix IDs on most of the older microarray chips begin with the prefix 'AFFX'.

You can safely remove these without worry.

To remove them:

Remove a subset of SNPs

To re-write the PED/MAP files, but with certain SNPs excluded, use the option

plink --file data --exclude mysnps.txt

where the file mysnps.txt is, as for the --extract command, just a list of SNPs, one per line. As described above, the --range command can modify the behaviour of --exclude in the same manner as for --extract.

[source: http://zzz.bwh.harvard.edu/plink/dataman.shtml#exclude]

Kevin

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written by Kevin Blighe Kevin Blighe

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