The frontline support team will be offline as we are occupied with the GATK Workshop on March 21st and 22nd 2019. We will be back and available to answer questions on the forum on March 25th 2019.

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.


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