vstol 0.4.1

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VSTOL

VSTOL (Variant Standardization, Tabulation, and Operations Library) is a toolkit that standardizes smalll and structural DNA variants from VCF files into the Occam's Variant Grammar TSV files. It also supports list operations (annotate, diff, intersect, merge, overlap) on variant lists.

01. Installation

vstol is available on pypi:

pip install vstol

02. Dependencies

• python>=3.10
• pandas>=2.0.3
• numpy>=1.22.3
• networkx>=3.4.2
• intervaltree>=3.1.0

03. Usage

vstol [-h] [--version] {annotate,diff,intersect,merge,overlap,vcf2tsv}

04. Available Commands

Command	Description
annotate	Annotate variants.
diff	Diff target variants from query variants.
intersect	Identify intersecting variants.
merge	Merge multiple variant lists into one list.
overlap	Identify variants that overlap with a list of genomic regions.
vcf2tsv	Convert a VCF file (see below for supported variant callers) to the Occam's Variant Grammar TSV file.

05. TSV File Headers

vstol vcf2tsv outputs each variant callset as a tab-separated values (TSV) file with the following columns:

• id
• source_id
• sample_id
• platform
• method
• chromosome_1
• position_1
• strand_1
• operation_1
• chromosome_2
• position_2
• strand_2
• operation_2
• sequence

Additional columns from the VCF file will be included.

06. Supported Variant Callers

To use VSTOL, we recommend that you first convert a VCF file to a TSV file using the vcf2tsv command in VSTOL. The following variant callers are currently supported:

• ClairS
• CuteSV
• DeepVariant
• Delly2
• GATK4 Mutect2
• Lumpy
• Manta
• PBSV
• Savana
• Severus
• Sniffles2
• Strelka2
• Svim
• SVision-pro