Alignment summary walker?

praveenrajs

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

Geraldine_VdAuwera

Hi Raj,

Check out our reimplementation of Samtools' Flagstat:

http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_FlagStat.html

praveenrajs

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.

Geraldine_VdAuwera

Unfortunately that's simply not a priority for us at this time, so we won't be able to do this anytime soon. However we welcome contributions from anyone including yourself who would like to implement this.

Kurt

Sounds like you want tools that can be found in the Picard suite. Check out "CollectAlignmentSummaryMetrics" and "CalculateHsMetrics"

http://picard.sourceforge.net/index.shtml