Alternatives and similar repositories for cyvcf2

Users that are interested in cyvcf2 are comparing it to the libraries listed below

• ryanlayer / samplot
  Plot structural variant signals from many BAMs and CRAMs
  ☆555Updated last year
• daler / pybedtools
  Python wrapper -- and more -- for BEDTools (bioinformatics tools for "genome arithmetic")
  ☆326Updated 7 months ago
• RealTimeGenomics / rtg-tools
  RTG Tools: Utilities for accurate VCF comparison and manipulation
  ☆326Updated 5 months ago
• igvteam / igv-reports
  Python application to generate self-contained pages embedding IGV visualizations, with no dependency on original input files.
  ☆385Updated this week
• dellytools / delly
  DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
  ☆488Updated 2 months ago
• Illumina / hap.py
  Haplotype VCF comparison tools
  ☆447Updated last year
• genome / bam-readcount
  Count bases in BAM/CRAM files
  ☆318Updated 3 years ago
• adamewing / bamsurgeon
  tools for adding mutations to existing .bam files, used for testing mutation callers
  ☆246Updated last year
• snakemake-workflows / dna-seq-gatk-variant-calling
  This Snakemake pipeline implements the GATK best-practices workflow
  ☆260Updated 2 years ago
• pezmaster31 / bamtools
  C++ API & command-line toolkit for working with BAM data
  ☆430Updated 5 months ago
• brentp / vcfanno
  annotate a VCF with other VCFs/BEDs/tabixed files
  ☆383Updated last month
• luntergroup / octopus
  Bayesian haplotype-based mutation calling
  ☆319Updated 3 weeks ago
• Illumina / strelka
  Strelka2 germline and somatic small variant caller
  ☆384Updated 3 years ago
• pyranges / pyranges
  Performant Pythonic GenomicRanges
  ☆489Updated last month
• pcingola / SnpEff
  ☆293Updated last month
• ACEnglish / truvari
  Structural variant toolkit for VCFs
  ☆384Updated 2 weeks ago
• Illumina / manta
  Structural variant and indel caller for mapped sequencing data
  ☆444Updated 2 weeks ago
• mskcc / vcf2maf
  Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms
  ☆401Updated 2 months ago
• lgmgeo / AnnotSV
  Annotation and Ranking of Structural Variation
  ☆263Updated 3 weeks ago
• dpryan79 / ChromosomeMappings
  This repository contains chromosome/contig name mappings between UCSC <-> Ensembl <-> Gencode for a variety of genomes.
  ☆243Updated 2 years ago
• saketkc / pysradb
  Package for fetching metadata and downloading data from SRA/ENA/GEO
  ☆344Updated this week
• bedops / bedops
  BEDOPS: high-performance genomic feature operations
  ☆352Updated 5 months ago
• hall-lab / speedseq
  A flexible framework for rapid genome analysis and interpretation
  ☆317Updated 3 years ago
• ga4gh / benchmarking-tools
  Repository for the GA4GH Benchmarking Team work developing standardized benchmarking methods for germline small variant calls
  ☆205Updated 4 years ago
• PapenfussLab / gridss
  GRIDSS: the Genomic Rearrangement IDentification Software Suite
  ☆277Updated 5 months ago
• fulcrumgenomics / fgbio
  Tools for working with genomic and high throughput sequencing data.
  ☆348Updated this week
• daler / gffutils
  GFF and GTF file manipulation and interconversion
  ☆308Updated last year
• lh3 / wgsim
  Reads simulator
  ☆282Updated 4 years ago
• FelixKrueger / Bismark
  A tool to map bisulfite converted sequence reads and determine cytosine methylation states
  ☆434Updated 2 months ago
• fritzsedlazeck / SURVIVOR
  Toolset for SV simulation, comparison and filtering
  ☆399Updated last year