VARIANT BENCHMARKING TOOLS (VBT)

Author: Berke Cagkan Toptas (berke.toptas@sbgdinc.com)
Project Language: C++11

VBT provides a set of tools that is used for aligner/variant calling benchmarking. VBT uses vcfeval as its core variant comparison library and htslib to read/write VCF and FASTA files.

Preprint of VBT is published at Biorxiv: Comparing complex variants in family trios

VBT contains 2 tool:

1. VARIANT COMPARISON
2. MENDELIAN VIOLATION DETECTOR

Installing VBT:

Using makefile:

VBT uses htslib as an external dependency and it needs to be installed before VBT. Please download the latest htslib version from htslib official page. After you download and extract htslib, you can install it using the following steps: (following steps are tested with htslib 1.6)

cd htslib-1.x
./configure
make
make install

You can download the latest version of VBT using the following git command:

git clone https://github.com/sbg/VBT-TrioAnalysis.git

Once you have successfully installed htslib and download VBT, Then you can use following commands to compile VBT:

cp -R (HTSLIB_PATH)/htslib (VBT_PATH)          //Copy htslib folder to VBT directory
cp (HTSLIB_PATH)/libhts.a (VBT_PATH)/lib       //Copy htslib binaries to VBT/lib 
cp (HTSLIB_PATH)/libhts.so (VBT_PATH)/lib      //Copy htslib binaries to VBT/lib
cp (HTSLIB_PATH)/libhts.so.2 (VBT_PATH)/lib    //Copy htslib binaries to VBT/lib
cd (VBT_PATH)                                  //Go inside the VBT folder where makefile is
make all                                       //Compile VBT

Using dockerfile:

You can run VBT as a docker image. A dockerfile is added to the project that is running on Ubuntu 14.04 instance.

cd (VBT_PATH)
docker build -t vbtapp:v1.0 .
docker run -ti vbtapp:v1.0

Note: If you are unable to compile program or getting runtime error, please contact me. (berke.toptas@sbgdinc.com)

Parameter format:

./vbt varComp [PARAMETERS]
./vbt mendelian [PARAMETERS]

For additional help, please use the following commands:

./vbt --help
./vbt [module_name] --help

Sample Execution (mendelian):

Example folder contains a minimal example for testing VBT mendelian. We placed chr21 of merged BWA+UG CEPH trio as an input VCF. For the FASTA file, we extract chr21 from GRCh37 reference. In order to run the sample test, following command can be executed :

./vbt mendelian -ref Example/human_g1k_v37_decoy_chr21.fasta -mother Example/UG_CEU_merged_cleaned_chr21.vcf -father Example/UG_CEU_merged_cleaned_chr21.vcf -child Example/UG_CEU_merged_cleaned_chr21.vcf -pedigree Example/ceu.ped -outDir <OUTPUT_DIRECTORY_FULL_PATH> -out-prefix ceu_21_sample --output-violation-regions

Important: VBT does not generate the output folder if it does not exist in the system due to support different operating systems. Please make sure that, your input directory already exists which is specified with -outDir parameter. Please refer to the mendelian page for additional parameter details.

This sample execution will produce:

1. ceu_21_sample_BestPathLogs.txt              //Logs of Best Path Algorithm
2. ceu_21_sample_ChildReportLog.txt            //Mendelian decision for Non-Ref child variants only
3. ceu_21_sample_DetailedLogs.txt              //Detailed human-readable logs of trio concordance analysis
4. ceu_21_sample_tab_delim_detailed_log.tsv    //Tab delimited version of detailed logs
5. ceu_21_sample_trio.vcf                      //Merged output trio (Mendelian decisions are annotated for each record)
6. ceu_21_sample_ViolationRegions.bed          //Violation regions in BED format (dedicated for de novo mutation analysis)

VBT Result Validation (mendelian):

We implemented a pipeline that evaluates Mendelian decisions of VBT against naive tools. You can find the details and the tools at Vbt Validation Pipeline folder.

Source Code Documentation:

A Doxygen html documentation is available for VBT under Doxygen folder.