SVTrek is a bioinformatics tool for auditing structural variation (SV) discoveries and can also perform SV discovery independently using long-read analysis.
SVTrek is written in C and utilizes the HTSlib library.
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
./svtrek [MODE] [OPTIONS]
SV discovery mode in graph alignment result. It requires input of GAF and GFA files.
./svtrek disc [-r|--gfa r/GFA] [-a|--gaf GAF] [OPTIONS]
-r, --gfa <r/GFA>- Specifies the GFA file to be processed.
-a, --gaf <GAF>- Specifies the GAF file to be used.
Variation auditing mode where it parses BAm file and validates the variations reported in VCF file.
./svtrek audt [-b|--bam BAM] [-v|--vcf VCF file] [OPTIONS]
-b, --bam <BAM>- Specifies the BAM file to be processed.
-v, --vcf <VCF file>- Specifies the VCF file to be used.
-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