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
Try this

 - https://www.biostars.org/p/13302/
 - https://www.biostars.org/p/51928/