VSTOL (Variant Standardization, Tabulation, and Operations Library) converts VCF files of small and structural variants to TSV files and facilitates list operations (anntoate, diff, filter, intersect, merge, overlap etc) on a variants list.
pip install . --verbose
- python>= 3.10
- pandas>=2.0.3
- numpy>=1.22.3
- maturin>=0.14,<0.15
- pysam
- rust
- r-base (>=4)
- dplyr (R package)
- ggplot2 (R package)
- optparse (R package)
vstol [-h] [--version] {annotate,diff,filter,intersect,merge,overlap,vcf2tsv,visualize}
| Command | Description |
|---|---|
| annotate | Annotate variant calls using pyensembl or gencode. |
| collapse | Collapse a variants list into unique variants. |
| compare | Compare two variants lists. |
| filter | Filter variant calls (can be used to identify somatic variants). |
| intersect | Identify intersecting variant calls. |
| merge | Merge variant calls from various variant callers. |
| overlap | Identify variants that overlap with a list of genomic ranges. |
| score | Calculates average alignment score for each breakpoint. |
| subtract | Identify variant calls specific to a list. |
| vcf2tsv | Convert a VCF file (see below for supported variant callers) to a TSV file. |
| visualize | Visualize a VSTOL TSV file |
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: