bam2wig - Convert bam files to wiggle files. Can be used to generate exonpart hints for AUGUSTUS.
bam2wig [-r region] [-t trackname] <in.bam>
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 'is sorted' " to check if the file is sorted.
AUGUSTUS was written by M. Stanke, O. Keller, S. König, L. Gerischer and L. Romoth.
An exhaustive documentation can be found in the file /usr/share/doc/augustus/README.md.gz.