sambamba-merge - tool for merging several BAM files into
one
sambamba merge OPTIONS <output.bam>
<input1.bam> <input2.bam> [...]
sambamba merge is used for merging several sorted BAM files
into one. The sorting order of all the files must be the same, and it is
maintained in the output file.
SAM headers are merged automatically like in Picard merging
tool.
- -t,
--nthreads=NTHREADS
- Specify number of threads to use for compression/decompression tasks.
- -l,
--compression-level=COMPRESSION_LEVEL
- Specify compression level of output file as a number from 0 to 9
- -H, --header
- Output only merged header to stdout in SAM format (e.g. for debugging
purposes). Other options are ignored.
- -p,
--show-progress
- Show progressbar in STDERR. For more information on the original samtools
MERGE behaviour, check out the [samtools
documentation](http://samtools.sourceforge.net/samtools.shtml