sambamba-markdup(1) -- 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.

