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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

INSTALLATION

Install dependencies

  • 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 install samtools libhts-dev

    • OR install HTSlib from https://github.com/samtools

        apt install -y samtools libbz2-dev liblzma-dev libncurses5-dev libssl-dev libcurl3-dev

  git clone https://github.com/samtools/htslib.git /path/where/HTSlib/reside
  cd /path/where/HTSlib/reside
  git submodule update --init --recursive
  autoreconf -i
  ./configure --prefix=/path/where/HTSlib/installed
  make
  make install

  export TOOLDIR=/path/where/HTSlib/installed

Compile

Once all dependencies are available, you can compile bam2wig using make.

  make

Test

Examples: A file tests/auxprogs/bam2wig/test_files/test.s.bam has been included.
You can try bam2wig by trying out the following examples:

  1. ./bam2wig test.s.bam
  2. ./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.