mcfonsecalab/variantutils repository overview

Dockerfile that includes a set of utilities for VCF manipulation/annotation.

• bcftools v1.18-13⁠ - BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF.
  docker run mcfonsecalab/variantutils:latest bcftools

• vt 0.5⁠ - vt is a variant tool set that discovers short variants from Next Generation Sequencing data.
  docker run mcfonsecalab/variantutils:latest vt

• plink v1.90b6.21⁠ - PLINK is a whole genome association variant analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.
  docker run mcfonsecalab/variantutils:latest plink

• plink2 v2.00a3.7⁠
  docker run mcfonsecalab/variantutils:latest plink2

• vcfanno v0.3.3⁠ - vcfanno allows to quickly annotate a VCF with any number of INFO fields from any number of VCFs or BED files.
  docker run mcfonsecalab/variantutils:latest vcfanno

• spliceai v1.3.1⁠ - A deep learning-based tool to identify variants altering the splicing.
  docker run mcfonsecalab/variantutils:latest spliceai

Python modules:

• cyvcf2 v0.30.22⁠ - Fast python VCF and BCF processing with cython and htslib.
  from cyvcf2 import VCF
  

• scikit-allel v1.3.6⁠ - Package that provides utilities for exploratory analysis of large scale genetic variation data. It is based on numpy, scipy, etc.
  import allel
  

• hgvs v1.5.4⁠ - hgvs - This package provides a Python library to parse, format, validate, normalize, and map sequence variants according to Variation Nomenclature (aka Human Genome Variation Society) recommendations.
  import hgvs.parser
  

Image latest version: 0.8
Last update: 10/09/2023

Update on v0.6: Version updates and manual compilation of bcftools and htslib utils, so that bcftools plugins can be used.
Update on v0.7: Version updates and removal of pyvcf package.
Update on v0.8: Version updates and addition of plink2 software.