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Illumina genotyping report to Plink files
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5.1 years ago
egustavsson • 10
Canada

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.

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

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5.1 years ago
egustavsson • 10
Canada

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

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