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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

1.3M 52 14
brentp
cyvcf2

cython + htslib == fast VCF and BCF processing

212K 440 77
hail-is
hail

Cloud-native genomic dataframes and batch computing

59K 1K 265
bihealth
vcfpy

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

40K 112 24
apriha
snps

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

10K 116 18
sbslee
fuc

Frequently used commands in bioinformatics

7K 58 8
helicalAI
helical

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

6K 214 37
ACEnglish
truvari

Structural variant toolkit for VCFs

4K 410 60
TRON-Bioinformatics
vafator

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

2K 10 0
varfish-org
mehari

Python bindings for the mehari variant annotator

2K 28 1
dbmi-bgm
granite-suite

A collection of software to work with genomic variants

1K 7 0
labsquare
cutevariant

GUI to visualize and process variant data

1K 108 22
vembrane
vembrane

vembrane filters, sorts, and transforms VCF records using python expressions

977 70 5
pwwang
vcfstats

Powerful statistics for VCF files

892 73 15
bihealth
varfish-cli

Command line interface client for VarFish Server.

877 2 2
pieetie
svforge

Synthetic VCF generator for structural variants (Manta, DELLY) with controlled variability and realistic artefact injection

838 1 0
remytuyeras
haplodynamics

A python library to develop genomic data simulators

618 4 0
aprilweilab
igdtools

Single-header C++ library for fast/low-memory VCF (Variant Call Format) parsing.

616 22 0
robertopreste
hmtnote

Human mitochondrial variants annotation using HmtVar.

613 18 1
bigbio
pypgatk

Python tools for proteogenomics

496 15 13
aehrc
variant-spark

machine learning for genomic variants

493 147 48
clintval
tp53

Tools for programmatically annotating VCFs with the Seshat TP53 database

431 1 0
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.

426 52 12
hail-is
j11hail

Cloud-native genomic dataframes and batch computing

414 1K 265
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