I have whole exome data for paired samples of blood and tumor for 23 patients. I processed them with BWA(alignment), Picard(removing duplicates, sorting), GATK(local realignment, base quality score re-calibration etc.), then ran MuTect with STD mode to identify somatic mutations.
I also have Sanger sequence results for 3 genes.
So I compared the results from whole exome and Sanger, and found that some somatic mutations identified from Sanger are not appearing in the results from whole exome data. I think I might need to modify some parameters when I run MuTect. Which parameter can I adjust?
I have attached some IGV figures in the regions where MuTect has missed somatic mutations. Some are too obvious, and cannot understand why MuTect does not identify them as mutation. The input to IGV is bam files from GATK base quality score recalibration.
Thank you very much for any advice, suggestions, or hints.