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.
vstol is available on pypi:
pip install vstol
- python>=3.10
- pandas>=2.0.3
- numpy>=1.22.3
- networkx>=3.4.2
- intervaltree>=3.1.0
vstol [-h] [--version] {annotate,diff,intersect,merge,overlap,vcf2tsv}
| 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. |
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.
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: