sambamba-flagstat(1)
flagstat - getting flag statistics from BAM file
Description
SAMBAMBA-FLAGSTAT
NAME
sambamba-flagstat - getting flag statistics from BAM file
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