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sambamba-flagstat(1) -- getting flag statistics from BAM file
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## SYNOPSIS
`sambamba flagstat` [OPTIONS] <input.bam>
## DESCRIPTION
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:
* duplicates
* mapped reads (plus percentage relative to the numbers from the first line)
* reads with 'is_paired' flag set
* paired reads which are first mates
* paired reads which are second mates
* paired reads with 'proper_pair' flag set (plus percentage relative to
the numbers of QC-passed/failed reads with 'is_paired' flag set)
* paired reads where both mates are mapped
* paired reads where read itself is unmapped but mate is mapped
* paired reads where mate is mapped to a different chromosome
* the same as previous but mapping quality is not less than 5
## OPTIONS
* `-t`, `--nthreads`=<NTHREADS>:
Specify number of threads to use for BAM decompression
* `-p`, `--show-progress`:
Show progressbar in STDERR
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