SVTrek

SVTrek is a bioinformatics tool for evaluating structural variation (SV) discoveries and can also perform SV discovery independently using long-read analysis.

Remarks

SVTrek is written in C and utilizes the HTSlib library.

Installation

Follow these steps to install SVTrek:

# clone the repository
git clone --recursive --depth 1 https://github.com/akmami/SVTrek.git

# install submodules
cd SVTrek
make install

# compile the program
make

Usage

./svtrek [-b|--bam BAM] [-v|--vcf VCF file] [OPTIONS]

Required Parameters

• -b, --bam <BAM>
  • Specifies the BAM file to be processed.
• -v, --vcf <VCF file>
  • Specifies the VCF file to be used.

Options

• -o, --output <filename>
  • Specifies the output filename.
  • Default: svtrek.out
• -t <num>
  • Number of threads to use for processing.
  • Default: 4
• --verbose
  • Enables verbose output.
  • Default: false
• --wider-interval <num>
  • Defines the offset interval for the start of the reads (DEL-START).
  • Default: 20000
• --median-interval <num>
  • Defines the offset interval for the start of the reads (INS).
  • Default: 10000
• --narrow-interval <num>
  • Defines the offset interval for the end of the reads (DEL-END).
  • Default: 2000
• --consensus-interval-range <num>
  • Specifies the offset that determines whether to consider the locations into the refinement.
  • Default: 500
• --consensus-interval <num>
  • Specifies the interval that determines whether reads are considered to be in the same position.
  • Default: 5
• --consensus-min-count <num>
  • Minimum number of elements required for consensus determination.
  • Default: 3

Example Usage

./svtrek -b input.bam -v input.vcf