Scroll to navigation

BAM2WIG(1)   BAM2WIG(1)

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

An exhaustive documentation can be found in the file /usr/share/doc/augustus/README.md.gz.