Targeted Exome Sequencing - what's the best approach after variant calling?

Question

[Rick P]

Hi all!

I have been dealing with a targeted exome analysis which have some particularities. I have some tumor (T) and matched normal (N) samples and the VCF files were given to me after variant calling using the Torrent Variant Caller plugin and an hotspot file.

I have done some comparison between the T and N VCF files in order to identify somatic mutations (extracting the GT info from the vcf file and using the diff bash command), although in terms of genotypes there are no relevant differences.

I'm struggling a bit because I am relatively new to this area of bioinformatics and I don't know what the next steps should be.