Is there a tool for calculating the number of uniquely mapped reads, ambigiously mapped reads, and unmapped reads from sam/bam?

Question

[O.rka]

I found a tool called MMQuant but this is suppose to be drop in replacement (though, it's not) for featureCounts. I'm trying to calculate the number of uniquely mapped reads, the number of ambigiously mapped reads, and the number of unmapped reads.

Is there a tool that can calculate these basic measures for sam/bam files?

[lieven.sterck]

why not just use featureCounts in the first place? (== might be useful to mention why do you want an alternative for it when asking for alternatives)

htseq-count ?

[O.rka]

I’m getting a large number of ambiguously mapped reads and a very inconsistent gene expression between replicates. I suspect it’s a result of these ambiguous reads. I want to know exactly what proportion of the read pairs are ambiguously mapped.

[O.rka]

I hadn't realized this information is in the summary output of featureCounts.

[cpad0112]

use combination of samtools and broad institute's website for flags

[GenoMax]

BBTools (reformat.sh has a number of stats options) for aligned data files.