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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


specify directory for temporary files; default is /tmp


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


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


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.