bam2wig

NAME

bam2wig - Convert bam files to wiggle files. Can be used to generate exonpart hints for AUGUSTUS.

SYNOPSIS

bam2wig [-r region] [-t trackname] <in.bam>

OPTIONS

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.

Parameters:

-r

Allows to specify a target region, e.g. 'chr3L:10-250' This option can only be used if an index file exists, see: samtools index

-t

string provided as track name

AUTHORS

AUGUSTUS was written by M. Stanke, O. Keller, S. König, L. Gerischer and L. Romoth.

ADDITIONAL DOCUMENTATION