Quick and easy way to get alignment stats from many SAM/BAM files?

Question

[goodez]

Is there a good tool for extracting basic alignment stats from multiple BAMs/SAMs? I have tried CollectAlignmentSummaryMetrics from Picard and I really don't like it.

I just want simple statistics such as:

SAMPLE, TOTAL READS, ALIGNED READS, UNIQUELY MAPPED READS

It would be best if this were output in a table format so I could plot the statistics for many samples.

I could try to make a custom script for this, but I feel like a good tool should be out there.

[ATpoint]

So I am not the only one who dislikes the Picard tools :-D

Answer 1

[GenoMax]

Simply using samtools stats?

[h.mon]

And samtools flagstat?

[goodez]

Thanks -- not sure how I didn't come across this

[WouterDeCoster]

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