Question: Illumina genotyping report to Plink files
1
gravatar for egustavsson
4.2 years ago by
egustavsson10
Canada
egustavsson10 wrote:

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.

 

 

conversion plink snp illumina • 4.6k views
ADD COMMENTlink modified 10 days ago by Biostar ♦♦ 20 • written 4.2 years ago by egustavsson10

https://github.com/nicolazzie/SNPChimpRepo

ADD REPLYlink written 2.5 years ago by forever80

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

ADD REPLYlink written 7 weeks ago by Phoenix Mu0
0
gravatar for egustavsson
4.2 years ago by
egustavsson10
Canada
egustavsson10 wrote:

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

 

ADD COMMENTlink written 4.2 years ago by egustavsson10
2
gravatar for Jimbou
4.2 years ago by
Jimbou690
Germany
Jimbou690 wrote:

Try this

Converting Illumina Raw Genotype Data Into Plink Ped Format

Formatting Beadstudio Final Report Into Plink

ADD COMMENTlink written 4.2 years ago by Jimbou690
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