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

Stephanie M. Gogarten sdmorris at u.washington.edu
Tue Jun 3 19:14:12 CEST 2014


Hi Abhi,

We have never started from the raw idat files.  My experience is limited 
to using B allele frequency and Log R Ratio (output from GenomeStudio 
along with the called genotypes) to detect large chromosome anomalies.

Stephanie

On 6/3/14 10:01 AM, Abhishek Pratap wrote:
> 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 at gmail.com <mailto:abhishek.vit at 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 at u.washington.edu <mailto:sdmorris at 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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