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Old 10-08-2012, 12:37 PM   #1
Location: baltimore

Join Date: Oct 2009
Posts: 89
Default bam file statistics

Is there any program to obtain detailed bam file statistics in addition to common stats such as:
# of total reads mapped.
# of total reads where read mapped and mate unmapped.
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Old 10-08-2012, 01:00 PM   #2
Richard Finney
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Location: bethesda

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check out samtools with flagstat option
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Old 10-08-2012, 02:30 PM   #3
Location: SW UK

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Have a look at Picard tools
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Old 10-09-2012, 01:02 AM   #4
Peter (Biopython etc)
Location: Dundee, Scotland, UK

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You can get some of that from 'samtools idxstats' (very fast - gets the counts from the BAM index file, *.bai), but not information about paired reads.
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