How to make .ped and .map files

Question

[s.labuschagne96]

Hello

I have a dataset but I need to create .ped and .map files (as I understand) in order to use plink to run a GWAS.

However, I do not know what files I need to use in order to create them, is there a file extension I need to look for?

The folders I have are :

phg000199.v1.CIDR_AlcoholDependence.genotype-original-submission.c1.ARC.set2.tar
phg000199.v1.CIDR_AlcoholDependence.raw-data-idat.c1.ARC.set3.tar

Inside phg000199.v1.CIDR_AlcoholDependence.genotype-original-submission.c1.ARC.set2.tar:

phg000199.v1.CIDR_AlcoholDependence.genotype-original-submission.c1.set2/[e-mail]
phg000199.v1.CIDR_AlcoholDependence.genotype-original-submission.c1.set2/[e-mail]
..

The inside of the files look like this:

[Header]
GSGT Version,1.7.4
Processing Date,11/16/2010 8:09 AM
Content,,HumanOmni1-Quad_v1-0_B.bpm
Num SNPs,1140419
Total SNPs,1140419
Num Samples,3198
Total Samples,3198
File ,2404 of 3198
[Data]
SNP Name,Sample Name,GC Score,Allele1 - Forward,Allele2 - Forward,Allele1 - Top,Allele2 - Top,Allele1 - Design,Allele2 - Design,Allele1 - AB,Allele2 - AB,Theta,R,X,Y,X Raw,Y Raw,B Allele Freq,Log R Ratio
200006,Yale_1126@0095478175,0.7684,C,C,G,G,G,G,B,B,0.973,1.662,0.068,1.593,1898,23337,0.9925,-0.1059
200052,Yale_1126@0095478175,0.9187,T,T,T,T,A,A,B,B,0.979,0.967,0.030,0.936,1348,15521,0.9957,0.0980
200053,Yale_1126@0095478175,0.5952,T,T,A,A,T,T,A,A,0.100,1.680,1.450,0.231,22068,3981,0.0009,0.1316
200070,Yale_1126@0095478175,0.9385,G,G,C,C,G,G,A,A,0.023,0.576,0.556,0.020,8707,1051,0.0040,0.2924
200078,Yale_1126@0095478175,0.6388,G,C,C,G,C,G,A,B,0.470,2.917,1.527,1.390,22964,19518,0.4306,0.0624
200087,Yale_1126@0095478175,0.7881,T,T,A,A,T,T,A,A,0.047,0.794,0.739,0.055,11387,1279,0.0000,-0.5111
200096,Yale_1126@0095478175,0.8539,A,C,A,C,A,C,A,B,0.436,1.335,0.735,0.600,11513,9146,0.5040,-0.1515
200124,Yale_1126@0095478175,0.8290,A,G,A,G,T,C,A,B,0.634,1.451,0.571,0.880,9160,13160,0.5002,0.2374
200199,Yale_1126@0095478175,0.9430,G,G,G,G,C,C,B,B,0.987,0.851,0.018,0.834,930,14867,0.9956,0.0831

[4galaxy77]

First, .ped and .map files are pretty outdated now, you should use --pgen/--pvar/--psam files instead. It seems like you've got 2 .csv files which is a very generic format, so we can't tell you how to convert them. Can you post a couple of lines of the unzipped .csv.gz file into your original question. TBH, I would go back to whoever gave you this data and ask for it in a proper format.

[s.labuschagne96]

@4galaxy77 I have done so and gotten rid of the other file contents