---
name: "sambamba-markdup"
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-markdup"
---

# sambamba-markdup(1)

finding duplicate reads in BAM file

## NAME

**sambamba-markdup** - finding duplicate reads in BAM file

## SYNOPSIS

**sambamba markdup** *OPTIONS* \<input.bam\> \<output.bam\>

## DESCRIPTION

Marks (by default) or removes duplicate reads. For determining whether a read is a duplicate or not, the same \`sum of base qualities´ method is used as in Picard *https://broadinstitute.github.io/picard/picard-metric-definitions.html*.

## OPTIONS

- **-r**, **--remove-duplicates**

  remove duplicates instead of just marking them

- **-t**, **--nthreads**=*NTHREADS*

  number of threads to use

- **-l**, **--compression-level**=*N*

  specify compression level of the resulting file (from 0 to 9)");

- **-p**, **--show-progress**

  show progressbar in STDERR

- **--tmpdir**=*TMPDIR*

  specify directory for temporary files; default is **/tmp**

- **--hash-table-size**=*HASHTABLESIZE*

  size of hash table for finding read pairs (default is 262144 reads); will be rounded down to the nearest power of two; should be **\> (average coverage) \* (insert size)** for good performance

- **--overflow-list-size**=*OVERFLOWLISTSIZE*

  size of the overflow list where reads, thrown away from the hash table, get a second chance to meet their pairs (default is 200000 reads); increasing the size reduces the number of temporary files created

- **--io-buffer-size**=*BUFFERSIZE*

  controls sizes of two buffers of BUFFERSIZE *megabytes* each, used for reading and writing BAM during the second pass (default is 128)

## SEE ALSO

Picard *https://broadinstitute.github.io/picard/picard-metric-definitions.html* metric definitions for removing duplicates.

## BUGS

External sort is not implemented. Thus, memory consumption grows by 2Gb per each 100M reads. Check that you have enough RAM before running the tool.