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=""> 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 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >