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:
1 maintainer
Metadata
1 maintainer
Release files for vstol 0.4.1
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| vstol-0.4.1.tar.gz | 27.8 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| vstol-0.4.1-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 96.8 kB
Release files / vstol-0.4.1.tar.gz
| Download URL | vstol-0.4.1.tar.gz |
|---|---|
| Size | 27.8 kB |
| Tags | Source |
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| Tags | Python 3 |
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| Uploaded via |
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