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=NTHREADSSpecify number of threads to use for BAM decompression
-p,--show-progressShow progressbar in STDERR