.\" generated with Ronn/v0.7.3
.\" http://github.com/rtomayko/ronn/tree/0.7.3
.
.TH "SAMBAMBA\-INDEX" "1" "2016-10-24" "" ""
.
.SH "NAME"
\fBsambamba\-index\fR \- tool for building standard index files for BAM data
.
.SH "SYNOPSIS"
\fBsambamba index\fR [\fB\-p\fR|\fB\-\-show\-progress\fR] [\fB\-t\fR|\fB\-\-nthreads\fR=NTHREADS] <input\.bam> [<output\.bai>]
.
.SH "DESCRIPTION"
\fBsambamba index\fR builds an index for a sorted by coordinate BAM file\. This step is required for effective region querying in most tools for working with BAM data\.
.
.P
An index is by default written to the file with the same filename except \fB\.bai\fR extension added to the end\. The user can, however, override this default by providing desired output filename explicitly as an optional command\-line argument\.
.
.SH "OPTIONS"
.
.TP
\fB\-p\fR, \fB\-\-show\-progress\fR
Show a wget\-like progressbar in STDERR\.
.
.TP
\fB\-t\fR, \fB\-\-nthreads\fR=\fINTHREADS\fR
Number of threads to use\.
.
.SH "EXAMPLES"
Build index file example\.bam\.bai given a sorted BAM file example\.bam:
.
.P
$ sambamba index example\.bam
.
.P
Build index file at custom location showing progress:
.
.P
$ sambamba index \-\-show\-progress example\.bam /tmp/example\.bam\.bai
.
.SH "SEE ALSO"
For more information on the original samtools INDEX behaviour, check out the samtools documentation \fIhttp://samtools\.sourceforge\.net/samtools\.shtml\fR
