sambamba-flagstat - getting flag statistics from BAM
file
sambamba flagstat OPTIONS <input.bam>
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
-