Make Ped And Map File For Plink Anlysis

Question

[mary]

Hello all, I am new in plink analysis, I have a data from Illumina chip 54k for bovine and I want to know how can I make a .PED and .MAP file from .csv file. you can see the first raw of my data in below

ARS-BFGL-BAC-10172 14 4736993 Plate10-H2 G G 0.025 0.895

ARS-BFGL-BAC-10172 14 4736993 Plate10-G2 A G 0.425 0.616

ARS-BFGL-BAC-10172 14 4736993 Plate10-A8 G G 0.014 0.905

ARS-BFGL-BAC-10172 14 4736993 Plate10-E1 A A 1.054 0.054

ARS-BFGL-BAC-10172 14 4736993 Plate9-D12 A G 0.548 0.739

please let me if anybody know

[Giovanni M Dall'Olio]

can you explain the meaning of the columns?

Answer 1

[Maxime Lamontagne]

You should try to make de lgen format (http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml#long).

You have 3 files to create.

MAP FILE http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml#map

Col 1: chromosome (1-22, X, Y or 0 if unplaced). I think it's your second column. 
Col 2: rs# or snp identifier. If you don't have it in your CSV file, wrote something like this with the chromosome and the position: 14.4736993. 
Col 3: Genetic distance (morgans). Replace by 0.
Col 4: Base-pair position (bp units). I think it's your third column.

FAM FILE ( first six columns of mydata.ped ) http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml#ped

Col 1: Family ID. If you don't have any family, use the same ID for Family and Individual.
Col 2: Individual ID.
Col 3: Paternal ID. Replace by 0 if you don't have any family.
Col 4: Maternal ID. Replace by 0 if you don't have any family.
Col 5: Sex (1=male; 2=female; other=unknown).
Col 6: Phenotype. It could be anything.

LGEN FILE http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml#long

It's the bigger one.

Col 1: family ID. Same one as the FAM file.
Col 2: individual ID. Same one as the FAM file.
Col 3: snp ID. Same one as the MAP file.
Col 4: allele 1 of this genotype. I think it's your column 5. 
Col 5: allele 2 of this genotype. I think it's your column 6.

I don't wrote any code but I thinks you sould be able to do it with R or shell command.

Answer 2

[mary]

Dear Baboune thank you so much for your reply. I make a map file but for fam I have problem.the thing that make me confuse is that I have familiy whit pedegree. I had one sire that mated with several dam so I dont know how can I write the family Id. for example I have a sire that mated with his sister or his mother so I dont know how I can make a fam file. in my data just sire be genotyped and we didnt genotyprd any dam. I will be appriciated if you guid me. You can see my data pedegree below

animal id paternal id maternal id sex
1972801 11788713 11809591 2
1973415 11797754 1972679 2
4641860 11798566 4641660 2

this show the identity ear number of bovine. And I have another file that refer me to plate identity. And another thing is that I have quantitative record, I dont know what can I put for phenotype colum.

thank you so much

[Maxime Lamontagne]

Phenotype Column: You can use quantitative value (http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml#ped). Just make sure you use a period and not a comma.

Family ID: I think it depends of your experimental design and the goal of your study. If you don't care, I suggest you use a unique Family ID for each paternal and maternal combination.

[mary]

dear Baboune thanks a lot for your suggestion , i try to do it chr by chr because of error ' FATAL ERROR Exhausted system memory ' . is there any way i do it chr bye chr.