PLINK .bim file shows chromosome 0 on Affymetrix chip

Question

[philipovic]

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

[Maxime Lamontagne]

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.

[always_learning]

Did you able to find out answer for this?

Answer 1

[mariaf.betancur]

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

[always_learning]

You can exclude them safely for further analysis.

[mariaf.betancur]

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

[always_learning]

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

Answer 2

[Leonida Monaco]

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?

[Maxime Lamontagne]

Did you try the --exclude option in PLINK?

[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?

[Kevin Blighe]

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

[Leonida Monaco]

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

[Kevin Blighe]

Good day to you too, Sir / Madam.

Answer 3

[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