Hi Dongchuan, whereas the UCSC Genome Browser is often the best choice for genomic data analysis, variant detection and annotation is an art in itself. You might have a look e.g. on Broad's Genome Analysis Toolkit, it includes modules for most standard analysis tasks, e.g. SNP calling, dbSNP removal and gene annotation: http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit#Variant_Evaluation_and_Manipulation_Tools
Don't hesitate to ask the mailing list if you have other questions, e.g. on how to display, filter, share or inspect SNPs or sequence read data. <http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit#Variant_Evaluation_and_Manipulation_Tools> cheers Max -- Maximilian Haussler Office:+44 161 27 55980 Mob: +44 7574 246 789 http://www.manchester.ac.uk/research/maximilian.haussler/ On Tue, Feb 8, 2011 at 10:26 PM, Guo, Dongchuan <[email protected]>wrote: > To whom it may concern, > > Currently, we perform an exom sequencing on samples from patients and tried > to identify the mutations that caused a genetic disorder. I just received > the exom sequencing data with about 700 candidate variants. The only > information of these variants are chromosome and physical location. I was > wondering if there were some ways that I could import the list of these > variants (chromosome and location) into UCSC browser and identified the > genes that variants were located and pull out the sequences flanking the > variants. Is there any esay way to tell if a variant cause synonymous, > nonsynonymous, or nonsense alterations? > > Thanks. > > Dongchuan Guo, PhD > Assistant Professor > Department of Internal Medicine > The University of Texas Medical School at Houston > Tel: 713-500-6849 > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
