sambamba-slice1
Copying a slice of bam file
Usage
sambamba slice
OPTIONS
<input.bam>
region
Overview
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
Releases
Unchanged in 3 releases since Debian 11 (Bullseye).