Then look at some of these position in IGV using the search box like this e.g. chr9:127534620


Let looks at the somatic and optionally germline calls in the IGV viewer.

Somatic:   

  * BRCA2 - [chr13 32339132](img/BRCA2_13_32339132.png)
  * TP53 - [chr17 7675088](img/TP53_17_7675088.png)


Investigate the variants, hover over the vcf and bam tracks to see the details of the calls.


Germline (use the original germline vcf file, not the filtered one so we have both samples in the same file):

  * BRCA1 - [chr17 43057078](img/BCRA1_chr17_43057078.png)