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# Alignment summary walker?

Member Posts: 5

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

Tagged:

Hi Raj,

Check out our reimplementation of Samtools' Flagstat:

Geraldine Van der Auwera, PhD

• Member Posts: 5

That does not help much. Looking for a detailed summary including uniquely mapped reads/% (on genome and/or target regions). My request is to extend the functionality of this walker to provide summary which would answer to most of the questions on alignment quality. I hope, you will consider this as a feature request.
Best, Raj.