om-annotsv-svc: Optical Mapping and AnnotSV Structural Variant Comparator

A software tool for comparison of structural variants identified by optical mapping technology (Bionano Genomics) and long-read next-generation sequencing technologies i.e. 10x Genomics, Oxford Nanopore Technologies and Pacific Biosciences. Structural variants produced by long-read next-generation sequencing technologies are analyzed using AnnotSV software tool. The tool employes distance variance between Bionano and AnnotSV genomic coordinates for the beginning and end of individual SVs. Various types of filtering, such as overlapping gene filter, variant type filter or distance variance filter can be used. The tool is provided as CLI application and is platform independent.

Current stable version

Current stable version is 1.0 - branch 1.0. Main/master branch is dedicated for further development and should not be used in production environment.

Requirements

Java Runtime Environment 8 or higher.

Command line arguments

Parameter	Long	Type	Default	Description	Required
-a	--annotsv_input	String		AnnotSV analysis result TSV file path.	*
-b	--bionano_input	String		Bionano Genomics analysis pipeline result SMAP file path.	*
-d	--variant_distance	Integer		Distance variance filter (i.e. number of bases difference between variant from OM and NGS/WGS)
-g	--gene_intersection	Boolean	false	Overlapping genes filter (i.e. variants with non-overlapping genes are filtered out)
-o	--output	String		Output result file path.	*
-t	--variant_type	String		Variant type filter. Any combination of BND,CNV,DEL,INS,DUP,INV,UNK.

Example of usage

Some basic example usage of structural variant comparator follows. More detailed usage with sample data and results are presented in sample package in ./example directory in this repository. Each directory in sample package contains README.txt file where can be found detailed description of each file. Runnable binary version of the application is presented in ./bin directory of the repository.

Basic usage

In basic setup application compares all SVs contained in AnnotSV and Bionano result files. No filters are applied here.

java -jar om-annotsv-svc.jar -a annotsv_result.tsv -b bionano_pipeline_result.smap -o result.csv

Variance distance filter

Following command filters out variants which have distance variance greater than 50000 bases.

java -jar ovm-annotsv-svc.jar -a annotsv_result.tsv -b bionano_pipeline_result.smap -d 50000 -o result.csv 

Overlapping genes filter

Following command filters out variants which have distance variance greater than 50000 bases and have no genes in overlap.

java -jar om-annotsv-svc.jar -a annotsv_result.tsv -b bionano_pipeline_result.smap -d 50000 -g -o result.csv 

Variant type filter

Following command will analyze only translocations (BND), deletions (DEL) and insertions (INS). Other variant types are ignored.

java -jar om-annotsv-svc.jar -a annotsv_result.tsv -b bionano_pipeline_result.smap -t "BND,DEL,INS" -o result.csv 

Contact

If you have any problem or questions about the software tool, please contact us.

Tomáš Novosád (tomas.novosad@vsb.cz)

Jakub Savara (jakub.savara@vsb.cz)