sambamba-flagstat1
Getting flag statistics from bam file
Usage
sambamba flagstat
OPTIONS
<input.bam>
Overview
Outputs some statistics drawn from read flags.
First line contains numbers of QC-passed and QC-failed reads. Then come pairs of numbers, the former for QC-passed reads, the latter for QC-failed ones:
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duplicates
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mapped reads (plus percentage relative to the numbers from the first line)
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reads with ´is_paired´ flag set
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paired reads which are first mates
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paired reads which are second mates
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paired reads with ´proper_pair´ flag set (plus percentage relative to the numbers of QC-passed/failed reads with ´is_paired´ flag set)
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paired reads where both mates are mapped
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paired reads where read itself is unmapped but mate is mapped
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paired reads where mate is mapped to a different chromosome
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the same as previous but mapping quality is not less than 5
Options
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-t, --nthreads=NTHREADS -
Specify number of threads to use for BAM decompression
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-p, --show-progress -
Show progressbar in STDERR