shao-group / bamkit

A tool to process bam/sam files

Overview

bamkit is a toolkit designed to analyze and process bam/sam files. More functions will be continuously added.

Installation

To install bamkit from the source code, you need to first download/compile htslib, setup the corresponding environmental variables, and then compile the source code of bamkit.

Install htslib

Download htslib (license) from (http://www.htslib.org/) with version 1.5 or higher. Choose a directory for installation and set the environment variable HTSLIB for that. For example, for Unix platforms, do the following:

export HTSLIB="/directory/to/your/htslib/install"

Use the following to build libhts.a:

autoheader
autoconf
./configure --disable-bz2 --disable-lzma --disable-gcs --disable-s3 --enable-libcurl=no --prefix=$HTSLIB
make
make install

Compile bamkit

The compilation of bamkit requires automake and autoconf packages. If they have not been installed, on linux platform, do the following:

sudo apt-get install autoconf
sudo apt-get install automake

bamkit might also requires other libraries, such as libz, depending on your system. Install them if you encounter errors when compiling.

After that run the script build.sh, which will generate the executable file src/src/bamkit.

Usage

The current version of bamkit supports the following functionalities:

./bamkit ts2XS <input.bam> <output.bam>

The ts tag (used in minimap2 aligner) will be transformed into XS tag (used in STAR, HISAT alingers) and the resuting alignments will be written to output.bam.

./bamkit count <input.bam>

A statistic will be returned about the input.bam, including the number of reads and basepairs aligned, etc.

./bamkit strand <input.bam>

A report about the strandness of the input.bam will be written to standard output.

./bamkit alignPairEval <input.bam> <groundTruth.bam>

This command is about evaluation of aligners(like STAR). input.bam is the result of aligner and groundTruth.bam is the ground truth based on output of flux simulator. Evaluation results of the aligner will be written to standard output.

./bamkit bridgeEval <input.coral.bam> <input.aligner.bam> <groundTruth.bam> <reference.gtf>

This command is about evaluation of aligners and tools that bridge paired reads(like coral). input.coral.bam is the result of coral, input.aligner.bam is the result of aligner and groundTruth.bam is the ground truth based on output of flux simulator. reference.gtf is the annotation used to simulate reads. Evaluation results of the aligner and coral will be written to standard output.