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Vcf Python Packages

Python packages with the GitHub topic vcf. Sorted by relevance, with stars and monthly downloads.
py-vobject
vobject

A full-featured Python package for parsing and creating iCalendar and vCard files

1.2M 52 14
brentp
cyvcf2

cython + htslib == fast VCF and BCF processing

209K 440 76
hail-is
hail

Cloud-native genomic dataframes and batch computing

92K 1K 264
bihealth
vcfpy

Python 3 library with good support for both reading and writing VCF

39K 112 24
sbslee
fuc

Frequently used commands in bioinformatics

7K 58 8
apriha
snps

tools for reading, writing, generating, merging, and remapping SNPs

7K 115 18
helicalAI
helical

A framework for state-of-the-art pre-trained bio foundation models on genomics and transcriptomics modalities.

7K 211 37
ACEnglish
truvari

Structural variant toolkit for VCFs

4K 407 60
TRON-Bioinformatics
vafator

Annotate variants in a VCF file with technical annotations from one or more BAMs

3K 10 0
varfish-org
mehari

Python bindings for the mehari variant annotator

2K 27 1
dbmi-bgm
granite-suite

A collection of software to work with genomic variants

2K 7 0
aprilweilab
igdtools

Tools for converting VCF to IGD files and processing them.

1K 21 0
aehrc
variant-spark

machine learning for genomic variants

1K 147 48
vembrane
vembrane

Filter VCF/BCF files with Python expressions.

1K 69 5
bihealth
varfish-cli

Command line interface client for VarFish Server.

1K 2 2
labsquare
cutevariant

A standalone and free application to explore genetics variations from VCF file

879 108 21
bigbio
pypgatk

Python tools for proteogenomics analysis toolkit

842 15 13
pwwang
vcfstats

Powerful statistics for VCF files

815 73 15
KalinNonchev
gnomad-db

Scalable SQLite database for fast querying of gnomAD variant annotations (allele frequency, depth, population metrics). Supports gnomAD v2-v4, WGS and WES.

790 52 12
pieetie
svforge

🛠️ Reproducible, traceable synthetic SV VCFs for testing what your pipeline does to them. Caller-shaped Manta and DELLY outputs, real gnomAD/ENCODE injection with self-verifying tags. Synthetic data only.

763 1 0
robertopreste
hmtnote

Human mitochondrial variants annotation using HmtVar.

657 18 1
hail-is
j11hail

Cloud-native genomic dataframes and batch computing

616 1K 264
remytuyeras
haplodynamics

A python library to develop genomic data simulators

528 4 0
EUCANCan
variant-extractor

Deterministic and standard extractor of SNVs, indels and structural variants (SVs) from VCF files.

447 7 1
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