Convert Illumina Final Report File To Plink

Question

[Kyle Oliveira]

I know there's another question along the same lines, but I suspect my situation is slightly different...

I have an Illumina Final Report file, but I don't have access to Illumina directly, so I have to work with the file I have or I have to request one with more columns from someone else. My Final Report files have these columns:

SNP Name
Sample ID
Allele1 - Top
Allele2 - Top
GC Score
Sample Name
Sample Group
Sample Index
SNP Index
SNP Aux
Allele1 - Forward
Allele2 - Forward
Allele1 - Design
Allele2 - Design
Allele1 - AB
Allele2 - AB
Allele1 - Plus
Allele2 - Plus
Chr
Position
GT Score
Cluster Sep
SNP
ILMN Strand
Customer
Strand
Top Genomic Sequence
Plus/Minus Strand
Theta
R
X
Y
X Raw
Y Raw
B Allele Freq
Log R Ratio
CNV Value
CNV Confidence

From reading other questions, I believe I need to produce three files: a .lgen, a .map, and a .fam. My main question is this, I suppose: which columns do I use to produce each file?

Thanks!

Answer 1

[Maxime Lamontagne]

##Map file:

Column 1 - Chr: Chr
Column 2 - SNP: SNP Name
Column 3 - Genetic distance: 0
Column 4 - Base-pair position: Position

##Lgen file:

Column 1 - Family ID: Sample Group
Column 2 - Individual ID: Sample ID
Column 3 - SNP: SNP Name
Column 4 - A1: Allele1 - Forward
Column 5 - A2: Allele2 - Forward

##Fam file:

Column 1 - Family ID: Sample Group
Column 2 - Individual ID: Sample ID
Column 3 - Paternal ID:  0 
Column 4 - Maternal ID:  0 
Column 5 - Sex:  0
Column 6 - Phenotype:  0

You should add sex and age to your fam file afterward. If you have some family, add Paternal and Maternal ID too.

I think you should be able to use these files with PLINK, but I can't be sure because I don't have any example.

[Kyle Oliveira]

Thanks, that helps a lot!