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Guided HOWTO on Variant Analysis in Case-Control studies:



Some Links that belong on this page (somewhere):

Methods
PGAEdu Website
Tools
Finding Putative Variants for Correlative Studies
  1. Sequence the gene of interest
  2. Use Phred/Phrap to identify SNPs
  3. Create a prettybase file
Analyze the sequence from Step 1.
  1. SNPper
  2. Prettybase Pipeline
Genotype the variants from Step 1.
  1. Run pybest to determine the minmium SNPs
  2. Genotype the mimimum set of variants on each sample in your case and control populations
Family-based analyses
  1. SAS
  2. Merlin ... ??
 
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