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.