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Question: help with analysis of genotyping data from Illumina HumanOmni5-4v1_B chip
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gravatar for Abhishek Pratap
4.5 years ago by
Abhishek Pratap160 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@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 > >> > >> _______________________________________________ > >> Bioconductor mailing list > >> Bioconductor@r-project.org > >> https://stat.ethz.ch/mailman/listinfo/bioconductor > >> Search the archives: > >> http://news.gmane.org/gmane.science.biology.informatics.conductor > >> > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
ADD COMMENTlink modified 4.5 years ago by Stephanie M. Gogarten570 • written 4.5 years ago by Abhishek Pratap160
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gravatar for Stephanie M. Gogarten
4.5 years ago by
University of Washington
Stephanie M. Gogarten570 wrote:
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 > >> > >> _______________________________________________ > >> Bioconductor mailing list > >> Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> > >> https://stat.ethz.ch/mailman/listinfo/bioconductor > >> Search the archives: > >> http://news.gmane.org/gmane.science.biology.informatics.conductor > >> > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > >
ADD COMMENTlink written 4.5 years ago by Stephanie M. Gogarten570
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