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.
-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
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HTSlib version 1.10 or higher
- For operating systems that provide a package libhts-dev 1.10 or later (like Ubuntu 20.04 and Debian 11):
sudo apt-get install samtools libhts-dev
See INSTALL.md for further details, especially for manual installation from sources or installation without root rights.
- For operating systems that provide a package libhts-dev 1.10 or later (like Ubuntu 20.04 and Debian 11):
Once all dependencies are available, you can compile bam2wig using make.
make
Examples:
A file tests/auxprogs/bam2wig/test_files/test.s.bam has been included.
You can try bam2wig by trying out the following examples:
./bam2wig test.s.bam./bam2wig -t "my_specified_track" -r chr3L test.s.bam
Example (2) can only be done if an index file for test.s.bam exists.
Do samtools index test.s.bam and a file "test.s.bam.bai" will be generated.