Hi Stephanie

Just wondering if your group has some experience with doing CNV analysis on
the same genotyping data. I have the raw idat files and tried crlmm package
but unfortunately it failed. I have emailed the developers and waiting for
hear back from them.

In the interim I was wondering if I can get some pointers on handling IDAT
files for doing CNV analysis.

Many Thanks!
-Abhi


On Thu, Jan 16, 2014 at 12:03 PM, Abhishek Pratap <abhishek.vit@gmail.com>
wrote:

> Thanks a lot Stephanie for your quick response. This is was very
> useful info. I will follow up with package specific questions if any.
>
> Cheers!
> -Abhi
>
> On Tue, Jan 14, 2014 at 1:54 PM, Stephanie M. Gogarten
> <sdmorris@u.washington.edu> wrote:
> > 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.
> >
> > Stephanie
> >
> >
> > 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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> >>
> >
>
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