'\" t
.\"     Title: bam2wig
.\"    Author: [see the "AUTHOR(S)" section]
.\" Generator: Asciidoctor 2.0.12
.\"      Date: 
.\"    Manual: \ \&
.\"    Source: \ \&
.\"  Language: English
.\"
.TH "BAM2WIG" "1" "" "\ \&" "\ \&"
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.SH "NAME"
bam2wig \- Convert bam files to wiggle files. Can be used to generate exonpart hints for AUGUSTUS.
.SH "SYNOPSIS"
.sp
\fBbam2wig\fP [\-r region] [\-t trackname] <in.bam>
.SH "OPTIONS"
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File needs to be sorted by Reference ID (i.e. target name)
Use "samtools sort <in.bam>" to such effect.
Use "samtools stats <in.bam> | grep \(aqis sorted\(aq " to check if the file is sorted.
.SS "Parameters:"
.sp
\fB\-r\fP
.RS 4
Allows to specify a target region, e.g. \(aqchr3L:10\-250\(aq
This option can only be used if an index file exists, see: samtools index
.RE
.sp
\fB\-t\fP
.RS 4
string provided as track name
.RE
.SH "AUTHORS"
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AUGUSTUS was written by M. Stanke, O. Keller, S. König, L. Gerischer and L. Romoth.
.SH "ADDITIONAL DOCUMENTATION"
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An exhaustive documentation can be found in the file /usr/share/doc/augustus/README.md.gz.