[BioC] help with analysis of genotyping data from Illumina HumanOmni5-4v1_B chip

Stephanie M. Gogarten sdmorris at u.washington.edu
Tue Jan 14 22:54:07 CET 2014

Hi Abhi,

1. The GWASTools package was designed for QC of precalled array data. 
See the "Data Cleaning" vignette for a recommended workflow.  You might 
also want to look at Laurie et al 2010 in Genetic Epidemiology 
(10.1002/gepi.20516), as the vignette implements the QC methods 
described therein.

2. I usually get the annotation file from Illumina (it would probably be 
called HumanOmni5-4v1_B.csv).  Your collaborators may have this file, or 
you could register with Illumina's website to download it.  It has rsID, 
chromosome, position, alleles, and probe sequences.

3. I don't know of a good way at the moment, but "export GWASTools 
objects as VCF" is going on my to-do list.  I recently used the un-slick 
way of PLINK file -> load in PLINK/SEQ -> export VCF.  You might also 
try creating a VariantAnnotation object from your data and using the 
writeVcf method.


On 1/14/14 11:19 AM, Abhishek Pratap wrote:
> Hi Guys
> We have recently obtained from precalled genotype data from our
> collaborators generated from the Illumina Human Omni5 array chip
> (HumanOmni5-4v1_B). The genotypes have already been called using the
> Illumina's Genome Studio.
> I being new to the array based genotyping data (coming from sequencing
> arena) would like to know the following.
> 1. What QC can be done on these genotype data files (200 sampled) to
> ascertain their quality and filter out the low quality calls.
> 2. Does bioconductor have a package for annotation of this chip
> HumanOmni5-4v1_B. I was not able to find "humanomni5quadv1bCrlmm" but
> not sure if that would give me the annotation on loci / SNP.
> 3.  Any existing slick way to create VCF files from these 200 genotype
> files. Our goal is to summarize the information in a single VCF across
> all the samples tagging the low quality ones.
> Many thanks!
> -Abhi
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