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

                                                   August 2014                              SAMBAMBA-FLAGSTAT(1)