Plink file coded in 1/2/3/4 - how do I convert to ACGT

Question

[devenvyas]

I downloaded a data set in Eigensoft's PACKEDANCESTRYMAP format (http://genetics.med.harvard.edu/reich/Reich_Lab/Datasets_files/EuropeFullyPublic.tar.gz). I used convertf to convert the files to map/ped files.

The files used multiple spaces instead of tabs, so I did some find/replaces in shell to get the files into proper format.

On each line of the map file, looks like this

1    Affx-13943225    0.020130    752566    G    A
1    Affx-14804912    0.022518    842013    T    G
1    Affx-15453076    0.024116    891021    G    A
1    Affx-15485777    0.024457    903426    C    T
1    Affx-15871758    0.025727    949654    A    G
1    Affx-3942202    0.026288    1018704    G    A
1    Affx-50004516    0.026665    1045331    G    A
1    Affx-3979904    0.026674    1048955    A    G
1    Affx-3995844    0.026711    1061166    C    T
1    Affx-4055225    0.028311    1108637    G    A

The last two columns are the two alleles at each site.

1 SA062 0 0 1 1 1 1 4 4 1 1 2 4 1 3 3 3 3 3 1 1 4 4 3 3 3 3 2 2 4 4 3 3 2 2 2 2 1 1 2 4 2 2 3 3 3 3 4 4 4 4 3 3 1 3 1 1 4 4 2 2 3 3 3 3 2 2 3 3 2 2 3 3 1 1 3 3 2 2 3 3 3 3 1 1 4 4 2 4 2 2 3 3 1 1 3 3 3 3 2 2 2 2 1 1 3 3 3

That is a bit of the first line of the ped file.

I wish to convert the data into a standard ACGT-coded Plink dataset. I was wondering if you know how this can be implemented.

[Maxime Lamontagne]

--make-bed --alleleACGT

http://pngu.mgh.harvard.edu/~purcell/plink/dataman.shtml

[devenvyas]

Getting the files into Plink is the first problem though

When I tried

plink --file release --recode --out releaseACGT

The result was

ERROR: Problem with MAP file line:
1    Affx-13943225    0.020130    752566    G    A

Any idea how to get Plink to accept the map?

[Maxime Lamontagne]

A map file do not have allelic information.

You could:

1) Remove the alleles from the map file

2) rewrite the file in binary format: --make-bed

3) change the alleles in the bim file or use the --update-alleles command