The purpose of this practical is to get you familiar with visualising 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.
.bam file /home/participant/Course_Materials/data/cell-line/HCC1143.mix1.n20t80.reheader.bam.bam file /home/participant/Course_Materials/data/cell-line/HCC1143.NORMAL.30x.compare.reheader.bam.vcf file containing variants called by Caveman for this tumour /normal pair /home/participant/Course_Materials/Day3/HCC1143_vs_HCC1143_BL.flagged.muts.vcfchr8:142486034, C -> T
chr14:106471685, G -> A
chr15:91537757, C -> G
chr22:38120429, T -> C
chr2:9983580, T -> C
chr1:9633452, G -> A
chr3:177090982, A -> G
chr15:68175783, A -> G
chr3:140281877, A -> C
chr4:22961617, A -> T