Hi everyone, I've been trying to search around for the documentation of Illumina microarray genotype reports (.txt format) as I would like to understand the meaning for each data field. But so far I could only found an article that explain some data fields but not all. The sample data fields from the report are as follow:
- 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
This is a genotype report from one of multiple samples. So far I've only found an article from Illumina that provide some of the data field info. I searched through different posts in biostars and saw that many people would try to convert the into Plink or VCF for further analysis. Is it possible to retrieve some information from the genotype reports without converting them into Plink or VCF?
I'm new to Microarray data analysis and recently only start to try to understand the genotype report content as requested, hence I jump straight into here without going through the whole workflow :'D Any replies and comments are appreciated, thanks in advance!
