NGS-Var2018 Exercise.7
From BITS wiki
[ Main_Page | Hands-on_introduction_to_NGS_variant_analysis-2018 | NGS-Var2018 Exercise.6 ]
Review variants and annotations in IGV
This is not an exercise, explore the data and see it by yourself
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 preferred 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 Broad Institute site for more information. (<http://www.broadinstitute.org/igv>).
- download the necessary data for IGV visualisation as a Zip file from HERE
- decompress the archive to a place of your choice
- Open IGV and set it to hg38
- load BAM and VCF data from the online files
OR load the data from the BITS server directly (if bandwidth allows) with File - "Load from URL..."
- https://data.bits.vib.be/pub/trainingen/NGSVAR2018/6_SnpEff/GATK.GermlineSNPsAndIndelsCaller/HG001_100pc.recalibrated.g.realigned.bam *(& .bam.bai)*
- https://data.bits.vib.be/pub/trainingen/NGSVAR2018/6_SnpEff/SnpEff/SnpEff_GATK_HG001_recalibrated_vartypes.vcf.gz *(& .gz.tbi)*
- A HG001 Gold set : https://data.bits.vib.be/pub/trainingen/NGSVAR2018/0_reference/NA12878_HG001-chr22_gold.vcf.gz (.tbi)
- Play with the data (eg navigate to chr22:15,000,000-20,000,000)
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-2018 | NGS-Var2018 Exercise.6 ]