Illumina genotyping report to Plink files

Question

[egustavsson]

I just received my genotyping report files from Illumina, with the locus summary file, and I want to convert the files to Plink files.

They came as CSV so I converted them to tab delimited (.txt) and wanted to use gcta to convert into map + ped. However, I get the map file but get an error ("segmentation error") when it tries to create the .ped

My locus summary file

Index   Name    Chr     Position        AA Freq AB Freq BB Freq Call Freq       Minor Freq      10% GC  50% GC
1       1:10002775-GA   1       10002775        0.00    0.00    1       1       0.00    0.4114687       0.4114687
2       1:100152282-CT  1       100152282       0.00    0.00    1       1       0.00    0.3868383       0.3868383
3       1:100154376-GA  1       100154376       0.00    0.00    1       1       0.00    0.4968892       0.4968892
4       1:100154844-CA  1       100154844       0.00    0.00    1       1       0.00    0.3769583       0.3769583

Genotyping report file

[Header]
GSGT Version    1.9.4
Processing Date 3/12/2015 2:17 PM
Content         MEGA_Consortium_15063755_B1.bpm
Num SNPs        1548495
Total SNPs      1705969
Num Samples     572
Total Samples   576
File    1 of 6
[Data]
SNP Name        Sample ID       Allele1 - Forward       Allele2 - Forward       GC Score        X       Y
1:10002775-GA   WG0238334-DNAA01_Control        G       G       0.4115  0.027   1.531
1:100152282-CT  WG0238334-DNAA01_Control        C       C       0.3868  0.072   1.651
1:100154376-GA  WG0238334-DNAA01_Control        G       G       0.4969  0.019   0.855

Is there any way of doing this? I would appreciate any suggestions.

Thank you

[forever]

https://github.com/nicolazzie/SNPChimpRepo

[Phoenix Mu]

Does segmentation error typically mean that there is not enough memory?

Answer 1

[Jimbou]

Try this

• Converting Illumina Raw Genotype Data Into Plink Ped Format
• Formatting Beadstudio Final Report Into Plink

Answer 2

[egustavsson]

Thanks! I had to create the .lgen by moving some rows from the initial report and then Plink worked fine for creating the .ped