Alternatives and similar repositories for PyVCF:

Users that are interested in PyVCF are comparing it to the libraries listed below

• brentp / cyvcf2
  cython + htslib == fast VCF and BCF processing
  ☆395Updated 7 months ago
• dellytools / delly
  DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
  ☆462Updated last month
• freebayes / freebayes
  Bayesian haplotype-based genetic polymorphism discovery and genotyping.
  ☆821Updated 2 months ago
• brentp / vcfanno
  annotate a VCF with other VCFs/BEDs/tabixed files
  ☆375Updated last year
• genome / bam-readcount
  Count bases in BAM/CRAM files
  ☆315Updated 3 years ago
• pezmaster31 / bamtools
  C++ API & command-line toolkit for working with BAM data
  ☆424Updated 9 months ago
• RealTimeGenomics / rtg-tools
  RTG Tools: Utilities for accurate VCF comparison and manipulation
  ☆316Updated 10 months ago
• daler / pybedtools
  Python wrapper -- and more -- for BEDTools (bioinformatics tools for "genome arithmetic")
  ☆319Updated last month
• mdshw5 / pyfaidx
  Efficient pythonic random access to fasta subsequences
  ☆468Updated 6 months ago
• ryanlayer / samplot
  Plot structural variant signals from many BAMs and CRAMs
  ☆541Updated 9 months ago
• hall-lab / speedseq
  A flexible framework for rapid genome analysis and interpretation
  ☆316Updated 2 years ago
• daler / gffutils
  GFF and GTF file manipulation and interconversion
  ☆299Updated last year
• deeptools / deepTools
  Tools to process and analyze deep sequencing data.
  ☆718Updated this week
• mskcc / vcf2maf
  Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms
  ☆386Updated 4 months ago
• pcingola / SnpEff
  ☆269Updated 2 months ago
• arq5x / poretools
  a toolkit for working with Oxford nanopore data
  ☆242Updated 2 years ago
• adamewing / bamsurgeon
  tools for adding mutations to existing .bam files, used for testing mutation callers
  ☆240Updated 6 months ago
• lh3 / wgsim
  Reads simulator
  ☆274Updated 3 years ago
• OpenGene / AfterQC
  Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
  ☆209Updated 4 years ago
• ga4gh / benchmarking-tools
  Repository for the GA4GH Benchmarking Team work developing standardized benchmarking methods for germline small variant calls
  ☆203Updated 4 years ago
• Illumina / hap.py
  Haplotype VCF comparison tools
  ☆427Updated last year
• FelixKrueger / Bismark
  A tool to map bisulfite converted sequence reads and determine cytosine methylation states
  ☆417Updated this week
• nservant / HiC-Pro
  HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
  ☆402Updated last year
• The-Sequence-Ontology / Specifications
  GFF and GVF specification documents
  ☆213Updated 10 months ago
• vcflib / vcflib
  C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings
  ☆643Updated this week
• TransDecoder / TransDecoder
  TransDecoder source
  ☆288Updated 6 months ago
• dpryan79 / ChromosomeMappings
  This repository contains chromosome/contig name mappings between UCSC <-> Ensembl <-> Gencode for a variety of genomes.
  ☆241Updated 2 years ago
• marcelm / cutadapt
  Cutadapt removes adapter sequences from sequencing reads
  ☆545Updated 3 weeks ago
• abyzovlab / CNVnator
  a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads
  ☆220Updated 3 years ago
• lindenb / jvarkit
  Java utilities for Bioinformatics
  ☆497Updated this week