Author: Berke Cagkan Toptas
Variant Comparison tool is written using the algorithm of vcfeval using this paper. Please see command line parameters below.
./vbt varcomp -called <called_vcf_file> -base <baseline_vcf> -ref <reference_fasta> -outDir <output_directory> [OPTIONAL PARAMETERS]
A single parameter mode which prints all parameter options to the console. (./vbt varComp --help)
A required parameter which specifies the baseline vcf file path. It supports both vcf.gz and vcf file formats.
A required parameter which specifies the query vcf file path. It supports both vcf.gz and vcf file formats.
A required parameter which specifies the reference FASTA file path. It should be in FASTA (.fa) format. A FASTA index file is not mandatory. The tool will automatically generate a FASTA index file (.fai) if it does not exist.
A required parameter which specifies the output directory for program/error logs and ga4gh output vcf file. In current version, in order not to damage multiplatform capability, directory should be created by user.
An optional parameter which specifies the way output will generated. SPLIT mode creates 4 vcf files(TPbase, TPcalled, FP, FN). GA4GH mode creates a single merged vcf file. Default value is SPLIT.
An optional parameter which changes comparison mode to Allele Matching
An optional parameter which is used to select sample name from baseline vcf file. By default, first sample is selected.
An optional parameter which is used to select sample name from called vcf file. By default, first sample is selected.
An optional parameter which is used to filter variants with given filter name. Filter name should be same in baseline and called variants. By default, PASS filtering is applied to the variants. In order to disable filtering, '-filter none' should be used.
An optional parameter which is used to select regions from VCF file.
An optional parameter which is used to eliminate all of INDELs and SVs from input vcf files.
An optional parameter which is used to eliminate all of SNPs and SVs from input vcf files.
An optional parameter which disables reference overlapping in variant comparison. Only one of overlapping variants will be placed to the True Positive variant set.
An optional parameter that prints the sync point list of two vcf file.
An optional parameter where in reference overlapping mode variants will be trimmed starting from the longest suffix first. By default, VBT is trimming prefix of alleles first.
An optional parameter to specify number of threads. Default value is 2
An optional parameter to specify the maximum size of path that core algorithm can store inside. Default value is 150,000.
An optional parameter to specify the maximum iteration count that core algorithm can decide to include/exclude variant. Default value is 10,000,000
An optional parameter to specify the maximum base pair length of variant to process. Default value is 1000. Variants larger than the base pair are filtered out.