Coverage of ROI on TruSight

[ramujana]

Hello,
i'm using Illumina TruSight Cancer panel and would like to get statastics how well was covered every gene/ROI. I'm using MiSeq Reporter for alignment and VarianStudio for variant (.vcf) annotation and filtering. Could anyone give simple idea how to know how well (an which regions in particular) was covered particular gene/ROI? i gues it should be stored somewhere in a files after the alignment, thanks,

[TiborNagy]

If ROI was defined in a BED or GFF file, Bedtools coverage can do this.