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)