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

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.

rna-seq alignment
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written by goodez goodez

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

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written by ATpoint ATpoint

1 answer

Simply using samtools stats?

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written by GenoMax GenoMax

And samtools flagstat?

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written by h.mon h.mon

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

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written by goodez goodez

If an answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted.
Upvote|Bookmark|Accept

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written by WouterDeCoster WouterDeCoster

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