GATK licensing moves to direct-through-Broad model -- read about it on the GATK blog

Alignment summary walker?

Hi,
Does GATK2 provide a walker/option to summarize the read alignment in a given BAM file? The summary including total reads, reads mapped/%, reads uniquely mapped/%, reads uniquely mapped with 0mm/%, reads mapped on-target/%, reads uniquely mapped on-target%, etc is of great use to assess the mapping quality for whole genome or targeted analysis.
Please advice me on how I can obtain this using any of the walkers available.
Thanks,
Raj

Answers

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