The purpose of this practical is to get you familiar with visualising somatic SNV calls in IGV, and to assess whether they are genuine calls or technical artefacts.
You might find this set of hints useful when assessing the calls.
This section uses a breast cancer genome that is publicly-available and well-characterised
It was used as part of the Cancer Research Uk Cambridge Institute Summer School “Analysis of Cancer Genomes”; the material for which can be accessed online. The files you will need for this section are available in the google drive (make sure to download the bai files that correspond to the bam files)
Open the IGV genome browser.
Load the Tumour .bam file HCC1143_subset.bam
Load the Normal .bam file HCC1143_BL_subset.bam
Load the .vcf file containing variants called by Caveman for this tumour /normal pair HCC1143_vs_HCC1143_BL.annot.muts.vcf.gz
Load from Server... from the File menu
dbSNP and Repeat Masker options within the Variation and Repeats annotations sectionAll but one of the following set of candidate somatic SNVs were called by CaVEMan. The VCF track shows whether the call was made by CaVEMan; hovering over the bar representing the call will bring up a tooltip with details of the SNV call including whether it was filtered.
Click on the IGV link for each variant in turn to navigate to that genomic location in the IGV browser. Review the read alignments supporting the variant and those in the region surrounding the variant to decide on your confidence in the call. Click on the Vote link to register your decision anonymously.
We will review the results in class to see if there is agreement in the calls!