Python 3 library with good support for both reading and writing VCF
☆111Oct 2, 2025Updated 5 months ago
Alternatives and similar repositories for vcfpy
Users that are interested in vcfpy are comparing it to the libraries listed below
Sorting:
- Prioritizing Copy Number Variants (CNV) using Phenotype and Gene Functional Similarity☆17Mar 10, 2022Updated 3 years ago
- NiPTUNE. A Python library for NIPT analyses.☆12Nov 22, 2021Updated 4 years ago
- cython + htslib == fast VCF and BCF processing☆430Feb 23, 2026Updated 2 weeks ago
- Simple matching of HTS samples based on HLA typing☆14Jan 4, 2017Updated 9 years ago
- Code used to process and analyze structural variants and short tandem repeat variants profiled in 719 deeply sequenced whole genomes as p…☆11Jun 25, 2019Updated 6 years ago
- Directly create a bigwig file with signal derived from a sorted and indexed bam file.☆11Jul 7, 2017Updated 8 years ago
- Deprecated, see https://labsyspharm.github.io/rnaseq/☆12Feb 28, 2019Updated 7 years ago
- paplot creates various dynamic and interactive reports for cancer genome analysis.☆26Feb 1, 2023Updated 3 years ago
- A Variant Call Format reader for Python.☆417Sep 22, 2023Updated 2 years ago
- Quality of life improvements for Bioinformatics in Python.☆31Feb 28, 2026Updated last week
- dv-trio provides a pipeline to call variants for a trio (father-mother-child) using DeepVariants [1]. Genomic Variant Calling Files (gVCF…☆11Feb 3, 2021Updated 5 years ago
- Basic UPD caller☆12Aug 23, 2021Updated 4 years ago
- do some exercise☆14Dec 2, 2025Updated 3 months ago
- Lightweight mosaic/somatic SV caller for long reads (WIP)☆35Oct 27, 2025Updated 4 months ago
- prioritize effects of variant annotations from VEP, SnpEff, et al.☆34Dec 10, 2024Updated last year
- A tool for fast and accurate summarizing of variant calling format (VCF) files☆61Dec 27, 2022Updated 3 years ago
- Generate an enhanced VCF files from ClinVar XML Full releases☆15Feb 23, 2026Updated 2 weeks ago
- LEGACY repository for SODAR Core, preserved for saving review-related issues. See "sodar-core" for the up-to-date repository.☆15Jun 1, 2022Updated 3 years ago
- An ultra-fast and efficient genomic tool for coverage calculation☆170Feb 9, 2026Updated last month
- Simple vcf parser, based on PyVCF☆48Dec 6, 2018Updated 7 years ago
- SMN1 copy-number and sequence variant analysis from next generation sequencing data☆23Feb 20, 2026Updated 2 weeks ago
- A modular annotation tool for genomic variants☆147Updated this week
- visualization tools for exon/junction coverage☆11Dec 30, 2019Updated 6 years ago
- ☆16Jan 15, 2025Updated last year
- Tandem repeat genotyping with long reads☆35Sep 23, 2025Updated 5 months ago
- Bedfile perturbation tool☆17Updated this week
- The Vertebrate Genomes Project Mitogenome Assembly Pipeline☆19Mar 26, 2023Updated 2 years ago
- liftover for python, made fast with cython☆96Oct 14, 2025Updated 4 months ago
- 📊Evaluating, filtering, comparing, and visualising VCF☆28Mar 9, 2023Updated 3 years ago
- REEV: Explanation and Evaluation of Variants☆11Mar 2, 2026Updated last week
- Process Illumina instrument data into SAM/BAM/CRAM files.☆10Updated this week
- Copy number estimation of highly duplicated sequences☆10Aug 15, 2017Updated 8 years ago
- PhenomeXcan: mapping the genome to the phenome through the transcriptome☆11Jun 28, 2020Updated 5 years ago
- Shiny app for geno-pheno catalog☆11Nov 4, 2022Updated 3 years ago
- ☆11Apr 3, 2023Updated 2 years ago
- ☆13Apr 18, 2022Updated 3 years ago
- VarFish: comprehensive DNA variant analysis for diagnostics and research☆52Mar 2, 2026Updated last week
- Location of public benchmarking; primarily final results☆18Feb 17, 2025Updated last year
- VisCap is an open flexible, software program targeted to clinical laboratories for inference and visualization of germline copy number va…☆22Dec 13, 2019Updated 6 years ago