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SVABA.md

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The installation and usage of SVABA

1. About

SvABA is a method for detecting structural variants in sequencing data using genome-wide local assembly

SVaba Installation Guide

Prerequisites

Before installing SVaba, ensure you have:

  • Git
  • A C++ compiler (GCC recommended)
  • Make
  • CMake (version 3.10 or higher)
  • HTSlib (version 1.16 recommended)

Step 1: Install HTSlib

HTSlib is a required dependency for SVaba. Here's how to install it in your user directory:

# Create a software directory
mkdir -p ~/software
cd ~/software

# Download HTSlib
wget https://github.com/samtools/htslib/releases/download/1.16/htslib-1.16.tar.bz2

# Extract the archive
tar -xjf htslib-1.16.tar.bz2
cd htslib-1.16

# Configure with user directory prefix
./configure --prefix=$HOME/.local

# Compile and install
make
make install

Step 2: Install CMake (if version < 3.10)

SVaba requires CMake version 3.10 or higher. If your system version is older:

# Create installation directory
cd ~/software
mkdir cmake_install
cd cmake_install

# Download CMake
wget https://github.com/Kitware/CMake/releases/download/v3.25.1/cmake-3.25.1.tar.gz

# Extract and enter directory
tar -xzf cmake-3.25.1.tar.gz
cd cmake-3.25.1

# Configure and install
./bootstrap --prefix=$HOME/.local
make
make install

# Add to PATH
echo 'export PATH=$HOME/.local/bin:$PATH' >> ~/.bashrc
source ~/.bashrc   # For bash users
# Or for fish shell users:
# fish_add_path $HOME/.local/bin

Step 3: Install SVaba

Now we can proceed with SVaba installation:

# Clone SVaba repository
git clone --recursive https://github.com/walaj/svaba
cd svaba

# Create and enter build directory
mkdir build
cd build

# Configure with CMake
cmake .. -DHTSLIB_DIR=$HOME/.local

# Compile
make

Step 4: Set Up Environment

To make SVaba accessible from anywhere, add it to your PATH:

For Bash users:

echo 'export PATH=/path/to/svaba/build:$PATH' >> ~/.bashrc
source ~/.bashrc

For Fish shell users:

fish_add_path /path/to/svaba/build

Testing the Installation

To verify your installation:

svaba --help

Basic Usage Example

# Run tumor/normal analysis on Chr22 with 4 cores
svaba -t tumor.bam -n normal.bam -k 22 -G ref.fa -a test_id -p 4

2. Usage

2.1 Assume that you've already index and sort the BAM file first, you also have a BWM indexed genome

bwa index -a bwtsw /projects/b1171/qgn1237/1_my_database/GRCh38_p13/GRCh38.p13.genome.fa

svaba run -t in.bam -p 8 -a your_tag -G /projects/b1171/qgn1237/1_my_database/GRCh38_p13/GRCh38.p13.genome.fa

2.2 Output files

SRR11951439_sort.var.vcf

python SVABA_steps_generator.py --bam input.bam --reference reference.fa --tag my_analysis

python SVABA_steps_generator.py --bam input.bam --reference reference.fa --tag my_analysis --threads 16 --mem 100G --time 24:00:00