sambamba-markdup1
Finding duplicate reads in bam file
Usage
sambamba markdup
OPTIONS
<input.bam>
<output.bam>
Overview
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)
Releases
Unchanged in 3 releases since Debian 11 (Bullseye).