Alternatives and similar repositories for PyVCF:

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

• Clinical-Genomics / genmod
  Annotate models of genetic inheritance patterns in variant files (vcf files)
  ☆79Updated this week
• AndersenLab / VCF-kit
  VCF-kit: Assorted utilities for the variant call format
  ☆126Updated 2 weeks ago
• gogetdata / ggd-recipes
  conda recipes for genomic data
  ☆85Updated 3 years ago
• Clinical-Genomics / chanjo
  Chanjo provides a better way to analyze coverage data in clinical sequencing.
  ☆50Updated 2 months ago
• Cibiv / Teaser
  A tool to benchmark mappers and different parameters within minutes
  ☆43Updated 5 years ago
• quinlan-lab / vcf2db
  create a gemini-compatible database from a VCF
  ☆56Updated 4 years ago
• ekg / fastahack
  utilities for indexing and sequence extraction from FASTA files
  ☆59Updated 3 years ago
• brentp / duphold
  don't get DUP'ed or DEL'ed by your putative SVs.
  ☆104Updated 4 years ago
• CGATOxford / cgat
  Do not use - please refer to our newest code: https://github.com/cgat-developers/cgat-apps
  ☆124Updated 6 years ago
• arq5x / bedtools-protocols
  ☆78Updated 11 years ago
• peterjc / picobio
  Miscellaneous Bioinformatics scripts etc mostly in Python
  ☆45Updated this week
• lh3 / fermi-lite
  Standalone C library for assembling Illumina short reads in small regions
  ☆72Updated 2 years ago
• NCBI-Hackathons / Community_Software_Tools_for_NGS
  ☆62Updated 8 years ago
• nhansen / SVanalyzer
  Tools for the analysis of structural variation in genomes
  ☆78Updated 11 months ago
• vplagnol / ExomeDepth
  ExomeDepth R package for the detection of copy number variants in exomes and gene panels using high throughput DNA sequencing data.
  ☆69Updated last month
• Clinical-Genomics / MIP
  Mutation Identification Pipeline. Read the latest documentation:
  ☆44Updated last year
• moonso / vcf_parser
  Simple vcf parser, based on PyVCF
  ☆46Updated 6 years ago
• Illumina / canvas
  Canvas - Copy number variant (CNV) calling from DNA sequencing data
  ☆126Updated 5 years ago
• PapenfussLab / StructuralVariantAnnotation
  R package designed to simplify structural variant analysis
  ☆72Updated 3 years ago
• lpryszcz / bin
  My bioinfo toolbox
  ☆49Updated last month
• RCollins13 / CNView
  Visualization and annotation of CNVs from population-scale whole-genome sequencing data
  ☆71Updated 7 years ago
• daler / metaseq
  Framework for integrated analysis and plotting of ChIP/RIP/RNA/*-seq data
  ☆87Updated 4 years ago
• andyrimmer / Platypus
  Platypus Variant Caller
  ☆108Updated 8 months ago
• ngsutils / ngsutils
  Tools for next-generation sequencing analysis
  ☆88Updated 5 years ago
• JohnLonginotto / pybam
  Very simple, pure python, BAM file reader
  ☆79Updated 6 years ago
• seppinho / mutserve
  mtDNA Variant Caller
  ☆34Updated 2 months ago
• arq5x / grabix
  a wee tool for random access into BGZF files.
  ☆84Updated 6 years ago
• mozack / abra
  Assembly Based ReAligner
  ☆73Updated 6 years ago
• lh3 / fermikit
  De novo assembly based variant calling pipeline for Illumina short reads
  ☆108Updated 4 years ago
• DaehwanKimLab / hisat
  Fast spliced aligner with low memory requirements
  ☆41Updated 9 years ago