What each column from Genotyping data is? (GWAS)

Question

[kkp5232]

Hello,

I am working with GWAS. I am new with this thing.. I know some columns but I don't know what some columns are. Do you have any good link that explain what each column is? And how did we find those number? For example, what is X for? How did we found X? What's about GC score? and few those 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

Thanks!

[zorbax]

Hi:

It looks like a configuration file for later analysis.

Btw, you provide few data.

this help you? Convert Illumina Final Report File To Plink

[kkp5232]

That link is similar idea but that did not give me an answer I look for.

I will work on the KEGG pathway with those SNPs. So I believe I will want to use GC score but I want to be clarification what those are.

Actually I have only:

SNP Name
Allele1 - Top
Allele2 - Top
GC Score
Sample Name
Allele1 - Forward
Allele2 - Forward
Allele1 - Design
Allele2 - Design
Allele1 - AB
Allele2 - AB
Theta
R
X
Y
X Raw
Y Raw
B Allele Freq
Log R Ratio

I used that list with more variables because I am curious what those are as well :) But this list is what I really have. I just want to make sure I understand this correctly. GC score is count of GC in the SNP string? Something like this, is there any source that will explains about each?

What do you means by "Btw, you provide few data"? Do you want me to provide the pseudo data?

Thank you for your response!