---
name: "sambamba-flagstat"
section: "1"
platform: "linux"
package: "sambamba"
version: "1.0.1+dfsg-2+b1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/sambamba-flagstat"
---

# sambamba-flagstat(1)

getting flag statistics from BAM file

## 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