NGS-Var2017 Exercise.7
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[ Main_Page | Hands-on_introduction_to_NGS_variant_analysis-2017 | NGS-Var2017 Exercise.6 ]
Review variants and annotations in IGV
IGV: The Interactive Genome Viewer
Some users may prefer other gene browsers and are welcome to keep using them but we chose IGV as their favorite genome viewer because
- IGV is well documented
- IGV contains links to precious public datasets including Encode and UCSC tacks and because it is easy to deploy, fast and robust.
- IGV supports a large number of standard formats that can be found on their information pages (<http://www.broadinstitute.org/igv/FileFormats>).
IGV will be used during the session and is not further documented here, please refer to the very extensive online help content on the 'omnipresent' Broad Institute site for more information. (<http://www.broadinstitute.org/igv>).
- Download the bundle for local IGV reviex from HERE
- decompress the archive to a place of your choice
- Open IGV and set it to hg19
- Load BAM and VCF data (the copy gzipped and indexed) in IGV
- Play with the data (eg navigate to chr21:28,315,821-28,315,861)
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Remember this is only 10% of the reads but calls from the 100%
download exercise files
Download exercise files here
Use the right application to open the files present in ex7-files
References:
[ Main_Page | Hands-on_introduction_to_NGS_variant_analysis-2017 | NGS-Var2017 Exercise.6 ]
