NAME¶

sambamba-slice - copying a slice of BAM file

SYNOPSIS¶

sambamba slice OPTIONS <input.bam> region

DESCRIPTION¶

Outputs reads overlapping specified region into new BAM file. (Default destination is STDOUT.) Input file must be coordinate-sorted and indexed.

While the same can be done with sambamba-view, that would be much slower due to a lot of compression/decompression work. Instead of naive method, sambamba-slice leverages knowledge about structure of BAM file and recompresses only a few BGZF blocks at the beginning and the end of the region, while the BGZF blocks in the middle are copied as is. As such, this tool doesn´t offer any options related to number of threads or compression level - most of the time is spent on I/O operations.

OPTIONS¶

-o, --output-filename=OUTPUTFILE

Name of output file