Sambamba documentation

NAME

sambamba-markdup - finding duplicate reads in BAM file

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

Marks (by default) or removes duplicate reads. For determining whether a read is a duplicate or not, the same criteria as in Picard are used.

-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)

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.