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.