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

Abhishek Pratap abhishek.vit at gmail.com
Tue Jan 14 20:19:06 CET 2014

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!

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