how can i call using WES in whole chr position?
I wonder about option of intervals to search all of somatic mutations between mormal.bam and tomor.bam in WES. I wanted to make calling data using WES. so I wrote mutect script without inervals option because I wated to see all of mutations in WES data. But there poped up the this messege : java.lang.IllegalArgumentException: Comparison method violates its general contract! please help me to solve this problem.