basic bam-readcount function in GATK?
I'm hoping to find a GATK solution to replace the use of bam-readcount in a pipeline.
For a given BAM, and a given position, I need to get the number of reads for each base (reference and alteration), as well as the overall read depth at that position.
If this functionality is present, pointers to the appropriate classes/methods would be greatly appreciated.
I apologize if this is an obvious question. This is my first rodeo.