Welcome to the Variant Classification and Visualization Tutorial!ΒΆ
Updated: February 7th, 2012
Level: Advanced
Packages: DNA-Seq Analysis, Power Seat
Contents: Jump to Table of Contents
This tutorial covers a comprehensive variant classification workflow for filtering variants, classifying variants according to position relative to a gene transcript, classifying variants according to the variant’s effect on the amino acid sequence, and visualizing variants of interest.
The data for this tutorial is taken from the Complete Genomics sample sequence data, see CGI Sequence Data. The starter project also contains the phenotype spreadsheet containing the population information, the ftp directory, and the HapMap sample name which is not the same as the CGI sample name.
Requirements
To complete this tutorial you will need to download and unzip the following starter project.
Download
Variant Classification Starter Project Download size: 22 MB compressed.
You will also need to download the following annotation tracks:
- ReferenceSequence-UCSC_GRCh_37_Homo_sapiens.idf: 899 MB Compressed
- 1kG_Phase1_EUR-Sites-2011_05-GHI_GRCh_37_Homo_sapiens.idf: 314 MB Compressed
- SNPs132 Common-UCSC_GRCh_37_Homo_sapiens.idf: 432 MB Compressed
Note
To download the annotation tracks, open SVS and go to Tools > Manage Annotation Tracks and click on Download From Network.... Select the three tracks listed above and click Download.
CAUTION: It will take a while to download these tracks!
Table of Contents
