plucky (1) sambamba-markdup.1.gz

Provided by: sambamba_1.0.1+dfsg-2build1_amd64 bug

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.

                                                  February 2015                              SAMBAMBA-MARKDUP(1)