genotyping according to the red/green intensity for illumina microarray?

Question

[jmzeng1314]

In fact, I've asked a similar question a few days ago, but there's no clear answer.

I've done some searching thing, now I got a little clear .

Firstly I downloaded 2 IDAT format files for a sample which is illumina genotype array.

by using R package illuminaio , I can process them to generate a human readable files,just like :

idatFile='ENCFF267GLV.idat'
idat <- readIDAT(idatFile)                                
names(idat)
idatData <- idat$Quants    
head(idatData);dim(idatData)

converting Binary idat files to plant txt just like below:

> head(idatData,50)
         Mean   SD NBeads
1600101  3506  948     11
1600103 18868 1994     14
1600105   591  446     15
1600107   621  550     14
1600111   541  266     16
1600113   884  465     15
1600119   628  369     13
1600121  1066  730     15
1600125   791  330     12
1600131   660  434      9
1600133  1002  648     14

so , what's the next , how can I get the genotype information according to the Mean,NBeads,SD value for each probe ?

I know how to annotate the probe, don't worry !

I know there's a CRLMM genotyping algorithm (Carvalho et al., 2007; Lin et al., 2008) , but it's too complex, I just want to know how to do it firstly.

you can just recommend a package for me ,and show me the usage

Answer 1

[NS]

Hi

Were you able to process the idat files and convert them into standardized format such as Plink or VCF ? I am struggling with the same thing and have no idea of how to convert idat/gtc files to plink format ? Please let me know if you found the solution.

Thanks

Answer 2

[Giulio Genovese]

You can use my own bcftools plugin gtc2vcf to convert GTC files to VCF

Then it is easy to convert a VCF file to PLINK format using best practices