I have a BAM file from human whole exome sequencing data. I am looking for a tool (Windows OS) that can calculate the coverage for specific gene output.
For instance, I am using VarAFT Tool. I can look at specific gene, let's say PKD2, and the tool can output coverage 1x (100%), coverage 5x (95.2%), coverage 10x (93.5%), coverage 20x (90.1%) and coverage 30x (82.7%).
I am trying to look for specifically coverage 15x so that I can make comparison with other papers but to no success. If anyone can recommend a tool that can be used on Windows OS and calculate specific gene at coverage 15x, please let me know.