Analyzing Illumina Infinium Omni5M Genotyping Data

Question

[Abhi]

Hey Guys

I have recently obtained some relatively older genotyping dataset based on Illumina's Infinium Omni 5m platform for about 200 samples. In summary I have never analyzed this type of data before coming from a sequencing arena, I would greatly appreciate if someone can point me to relevant docs/ bioconductor packages.

here is what I am trying to do.

1. analyze SNPs/genotypes across 200 odd samples
2. filter out the low quality calls
3. have a single file (may be a VCF) where SNPs are summarized for all the samples.

Many Thanks! -Abhi

[331885030]

Hello, Do you have the Omni5M Genotyping data for the Sample NA12878? Thanks

Answer 1

[mazzottidr]

Do you have cases and controls? Despite the relatively small sample size, if you are interested in performing a GWAS, I would recommend plink (http://pngu.mgh.harvard.edu/~purcell/plink/).

Any particular interest in generating VCF calls? Are you willing to compare with NGS data?

[Abhi]

In this case we not aiming for standard GWAS as you rightly pointed the sample size is pretty low. You also guessed it right the plan is to integrate it with another datasets coming from NGS assays via VCF.