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The Top 23 Python Vcf Open Source Projects

Open source projects categorized as Python Vcf
Hail ⭐ 905
Cloud-native genomic dataframes and batch computing
dependent packages 17total releases 146most recent commit 3 months agopypi hail} Downloads
Samplot ⭐ 458
Plot structural variant signals from many BAMs and CRAMs
total releases 3most recent commit 5 months ago
Igv Reports ⭐ 298
Python application to generate self-contained pages embedding IGV visualizations, with no dependency on original input files.
total releases 25most recent commit 4 months ago
Genomics_general ⭐ 279
General tools for genomic analyses.
most recent commit 3 months ago
Pygeno ⭐ 242
Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs
total releases 18most recent commit 4 years ago
Kipoi ⭐ 222
Kipoi's model zoo API
dependent packages 7total releases 73most recent commit 9 months agopypi kipoi} Downloads
Vcf2phylip ⭐ 216
Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis
most recent commit 10 months ago
Somaticseq ⭐ 185
An ensemble approach to accurately detect somatic mutations using SomaticSeq
total releases 1most recent commit 6 months ago
Hgvs ⭐ 142
HGVS variant name parsing and generation
most recent commit 4 years ago
Sigprofilerextractor ⭐ 132
SigProfilerExtractor allows de novo extraction of mutational signatures from data generated in a matrix format. The tool identifies the number of operative mutational signatures, their activities in each sample, and the probability for each signature to cause a specific mutation type in a cancer sample. The tool makes use of SigProfilerMatrixGenerator and SigProfilerPlotting.
dependent packages 3total releases 50most recent commit 5 months agopypi SigProfilerExtractor} Downloads
Gcp Variant Transforms ⭐ 114
GCP Variant Transforms
most recent commit 2 years ago
Clinvar ⭐ 108
This repo provides tools to convert ClinVar data into a tab-delimited flat file, and also provides that resulting tab-delimited flat file.
most recent commit 4 years ago
Easysfs ⭐ 108
Effective selection of population size projection for construction of the site frequency spectrum. Convert VCF to dadi/fastsimcoal style SFS for demographic analysis
most recent commit 7 months ago
Vcf Kit ⭐ 107
VCF-kit: Assorted utilities for the variant call format
total releases 18most recent commit 8 months ago
Ngscheckmate ⭐ 106
Software program for checking sample matching for NGS data
most recent commit 8 months ago
Yhaplo ⭐ 98
Identifying Y-chromosome haplogroups in arbitrarily large samples of sequenced or genotyped men
most recent commit 3 months ago
Neopredpipe ⭐ 93
Neoantigens prediction pipeline for multi- or single-region vcf files using ANNOVAR and netMHCpan.
most recent commit 7 months ago
Pipeline Structural Variation ⭐ 87
Pipeline for calling structural variations in whole genomes sequencing Oxford Nanopore data
most recent commit 3 years ago
Svim ⭐ 85
Structural Variant Identification Method using Long Reads
total releases 19most recent commit 3 years ago
Cutevariant ⭐ 85
A standalone and free application to explore genetics variations from VCF file
total releases 40most recent commit 8 months ago
Parliament2 ⭐ 83
Runs a combination of tools to generate structural variant calls on whole-genome sequencing data
most recent commit 3 years ago
Snps ⭐ 82
tools for reading, writing, merging, and remapping SNPs
dependent packages 2total releases 42most recent commit 3 months agopypi snps} Downloads
Tiledb Vcf ⭐ 79
Efficient variant-call data storage and retrieval library using the TileDB storage library.
most recent commit 3 months ago
The 10 Most Depended On Python Vcf Open Source Projects
Hail ⭐ 905
Cloud-native genomic dataframes and batch computing
dependent packages 17total releases 146latest release October 30, 2023most recent commit 3 months agopypi hail} Downloads
Vcfpy ⭐ 78
Python 3 library with good support for both reading and writing VCF
dependent packages 17total releases 24latest release November 28, 2022most recent commit 4 months agopypi vcfpy} Downloads
Kipoi ⭐ 222
Kipoi's model zoo API
dependent packages 7total releases 73latest release June 14, 2022most recent commit 9 months agopypi kipoi} Downloads
Terra Notebook Utils ⭐ 6
Utilities for the Terra notebook environment.
dependent packages 5total releases 25latest release July 31, 2023most recent commit 9 months agopypi terra-notebook-utils} Downloads
Fuc ⭐ 38
Frequently used commands in bioinformatics
dependent packages 2total releases 44latest release September 09, 2023most recent commit 8 months agopypi fuc} Downloads
Snps ⭐ 82
tools for reading, writing, merging, and remapping SNPs
dependent packages 2total releases 42latest release June 06, 2022most recent commit 3 months agopypi snps} Downloads
Genotype ⭐ 7
Simple genotype comparison of VCF files
dependent packages 1total releases 9latest release September 23, 2020most recent commit a year agopypi genotype} Downloads
Vcf_parser ⭐ 32
Simple vcf parser, based on PyVCF
dependent packages 1total releases 49latest release November 01, 2016most recent commit 5 years agopypi vcf_parser} Downloads
Svtyper ⭐ 78
Bayesian genotyper for structural variants
dependent packages 1total releases 4latest release September 04, 2019most recent commit 4 years agopypi svtyper} Downloads
The 10 Latest Releases In Python Vcf Open Source Projects
Rnaindel ⭐ 20
Somatic indel discovery tool for tumor RNA-Seq data.
total releases 22latest release November 27, 2023most recent commit 3 months ago
Hail ⭐ 905
Cloud-native genomic dataframes and batch computing
dependent packages 17total releases 146latest release October 30, 2023most recent commit 3 months agopypi hail} Downloads
Introgression Detection ⭐ 31
total releases 24latest release October 16, 2023most recent commit 4 months ago
Vcfstats ⭐ 48
Powerful statistics for VCF files
total releases 15latest release September 27, 2023most recent commit 6 months ago
Fuc ⭐ 38
Frequently used commands in bioinformatics
dependent packages 2total releases 44latest release September 09, 2023most recent commit 8 months agopypi fuc} Downloads
Pypgx ⭐ 49
A Python package for pharmacogenomics (PGx) research
total releases 138latest release August 25, 2023most recent commit 4 months ago
Tb_variant_filter ⭐ 5
A tool for filtering VCF files (relative to M. tuberculosis H37Rv)
total releases 7latest release August 10, 2023most recent commit 5 months ago
Terra Notebook Utils ⭐ 6
Utilities for the Terra notebook environment.
dependent packages 5total releases 25latest release July 31, 2023most recent commit 9 months agopypi terra-notebook-utils} Downloads
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