NGS-Var2020 Exercise.7

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[ Main_Page | Hands-on_introduction_to_NGS_variant_analysis-2020 | NGS-Var2020 Exercise.6 ]


Review variants and annotations in IGV


igv-logo.png

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
ex7_01.png
  • load BAM and VCF data from the decompressed files

OR load the data from the BITS server directly (if bandwidth allows) with File - "Load from URL..."

ex7_02.png

  * Our BAM data : https://data.bits.vib.be/pub/trainingen/NGSVAR2020/2_mappings/HG001_10pc.recalibrated.bam (.bai)

  * Our variant data : https://data.bits.vib.be/pub/trainingen/NGSVAR2020/6_SnpEff/SnpEff_GATK_variants-full.recalibrated.vartypes.dbsnp.vcf.gz (.tbi)

Handicon.png Remember this is only 10% of the reads but VCF calls were made on the 100%

  * A HG001 Gold set : https://data.bits.vib.be/pub/trainingen/NGSVAR2020/0_reference/NA12878_HG001-chr22_gold.vcf.gz (.tbi)

  • Play with the data (eg navigate to chr22:15,000,000-20,000,000)
ex7_03.png


 

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-2020 | NGS-Var2020 Exercise.6 ]