Man page - sambamba-slice(1)

Packages contains this manual

Package:  sambamba
apt-get install sambamba

Manuals in package:
• sambamba-flagstat(1)
• sambamba-slice(1)
• sambamba-index(1)
• sambamba-view(1)
• sambamba-markdup(1)
• sambamba(1)
• sambamba-merge(1)
• sambamba-sort(1)
• sambamba-pileup(1)
Documentations in package:
• sambamba

Manual

SAMBAMBA-SLICE

NAME
SYNOPSIS
DESCRIPTION
OPTIONS

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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

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