# VSTOL
VSTOL (**V**ariant **S**tandardization, **T**abulation, and **O**perations **L**ibrary) is a toolkit that
standardizes smalll and structural DNA variants from VCF files into the [Occam's Variant Grammar](https://pirlblog.substack.com/p/variant-standardization)
TSV files. It also supports list operations (*annotate*, *diff*, *intersect*, *merge*, *overlap*) on variant lists.
[](https://github.com/pirl-unc/vstol/actions/workflows/main.yml)
[](https://opensource.org/licenses/Apache-2.0)
## 01. Installation
`vstol` is available on [pypi](https://pypi.org/project/vstol/):
```
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](https://github.com/HKU-BAL/ClairS)
- [CuteSV](https://github.com/tjiangHIT/cuteSV)
- [DeepVariant](https://github.com/google/deepvariant)
- [Delly2](https://github.com/dellytools/delly)
- [GATK4 Mutect2](https://gatk.broadinstitute.org/hc/en-us/articles/360035531132--How-to-Call-somatic-mutations-using-GATK4-Mutect2)
- [Lumpy](https://github.com/arq5x/lumpy-sv)
- [Manta](https://github.com/Illumina/manta)
- [PBSV](https://github.com/PacificBiosciences/pbsv)
- [Savana](https://github.com/cortes-ciriano-lab/savana)
- [Severus](https://github.com/KolmogorovLab/Severus)
- [Sniffles2](https://github.com/fritzsedlazeck/Sniffles)
- [Strelka2](https://github.com/Illumina/strelka)
- [Svim](https://github.com/eldariont/svim)
- [SVision-pro](https://github.com/songbowang125/SVision-pro)
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"description": "# VSTOL\nVSTOL (**V**ariant **S**tandardization, **T**abulation, and **O**perations **L**ibrary) is a toolkit that \nstandardizes smalll and structural DNA variants from VCF files into the [Occam's Variant Grammar](https://pirlblog.substack.com/p/variant-standardization) \nTSV files. It also supports list operations (*annotate*, *diff*, *intersect*, *merge*, *overlap*) on variant lists.\n\n[](https://github.com/pirl-unc/vstol/actions/workflows/main.yml)\n[](https://opensource.org/licenses/Apache-2.0)\n\n## 01. Installation\n\n`vstol` is available on [pypi](https://pypi.org/project/vstol/):\n```\npip install vstol\n```\n\n## 02. Dependencies\n- python>=3.10\n- pandas>=2.0.3\n- numpy>=1.22.3\n- networkx>=3.4.2\n- intervaltree>=3.1.0\n\n## 03. Usage\n\n```\nvstol [-h] [--version] {annotate,diff,intersect,merge,overlap,vcf2tsv}\n```\n\n## 04. Available Commands\n\n| Command | Description |\n|-----------|-------------------------------------------------------------------------------------------------------|\n| annotate | Annotate variants. |\n| diff | Diff target variants from query variants. |\n| intersect | Identify intersecting variants. |\n| merge | Merge multiple variant lists into one list. |\n| overlap | Identify variants that overlap with a list of genomic regions. |\n| vcf2tsv | Convert a VCF file (see below for supported variant callers) to the Occam's Variant Grammar TSV file. |\n\n## 05. TSV File Headers\n\n`vstol vcf2tsv` outputs each variant callset as a tab-separated values (TSV) file with the following columns:\n\n* id\n* source_id\n* sample_id\n* platform\n* method\n* chromosome_1\n* position_1\n* strand_1\n* operation_1\n* chromosome_2\n* position_2\n* strand_2\n* operation_2\n* sequence\n\nAdditional columns from the VCF file will be included.\n\n## 06. Supported Variant Callers\n\nTo use `VSTOL`, we recommend that you first convert a VCF file to a TSV file \nusing the `vcf2tsv` command in `VSTOL`. The following variant callers are currently supported:\n\n- [ClairS](https://github.com/HKU-BAL/ClairS)\n- [CuteSV](https://github.com/tjiangHIT/cuteSV)\n- [DeepVariant](https://github.com/google/deepvariant)\n- [Delly2](https://github.com/dellytools/delly)\n- [GATK4 Mutect2](https://gatk.broadinstitute.org/hc/en-us/articles/360035531132--How-to-Call-somatic-mutations-using-GATK4-Mutect2)\n- [Lumpy](https://github.com/arq5x/lumpy-sv)\n- [Manta](https://github.com/Illumina/manta)\n- [PBSV](https://github.com/PacificBiosciences/pbsv)\n- [Savana](https://github.com/cortes-ciriano-lab/savana)\n- [Severus](https://github.com/KolmogorovLab/Severus)\n- [Sniffles2](https://github.com/fritzsedlazeck/Sniffles)\n- [Strelka2](https://github.com/Illumina/strelka)\n- [Svim](https://github.com/eldariont/svim)\n- [SVision-pro](https://github.com/songbowang125/SVision-pro)\n",
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