bam file statistics

[adrian]

Hi:
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.
thanks
Adrian

[Richard Finney]

check out samtools with flagstat option

[swNGS]

Have a look at Picard tools

[maubp]

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.