Man page - sambamba-flagstat(1)

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Package:  sambamba
apt-get install sambamba

Manuals in package:
• sambamba-flagstat(1)
• sambamba-slice(1)
• sambamba-index(1)
• sambamba-view(1)
• sambamba-markdup(1)
• sambamba(1)
• sambamba-merge(1)
• sambamba-sort(1)
• sambamba-pileup(1)
Documentations in package:
• sambamba

Manual

SAMBAMBA-FLAGSTAT

NAME
SYNOPSIS
DESCRIPTION
OPTIONS

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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

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