Top 13 Vcf Open-Source Projects

• Hail

  5 938 9.8 Python

  Cloud-native genomic dataframes and batch computing

  

• htslib

  7 776 8.9 C

  C library for high-throughput sequencing data formats

  

Project mention: Gentoo -Os vs -O3 application startup time? | /r/Gentoo | 2023-06-29

• InfluxDB

  www.influxdata.com featured

  Power Real-Time Data Analytics at Scale. Get real-time insights from all types of time series data with InfluxDB. Ingest, query, and analyze billions of data points in real-time with unbounded cardinality.

  

• snippy

  6 437 3.9 Perl

  :scissors: :zap: Rapid haploid variant calling and core genome alignment

• hap.py

  2 394 0.0 C++

  Haplotype VCF comparison tools

  

• cyvcf2

  1 358 7.7 Cython

  cython + htslib == fast VCF and BCF processing

• vcf2maf

  2 356 0.0 Perl

  Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms

  

• truvari

  1 292 9.2 Python

  Structural variant toolkit for VCFs

  

• SaaSHub

  www.saashub.com featured

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• genozip

  2 149 9.1 C

  A modern compressor for genomic files (FASTQ, SAM/BAM/CRAM, VCF, FASTA, GFF/GTF/GVF, 23andMe...), up to 5x better than gzip and faster too

• gw

  2 137 9.5 C++

  Genome browser and variant annotation

• TileDB-VCF

  4 80 8.6 C++

  Efficient variant-call data storage and retrieval library using the TileDB storage library.

  

• vembrane

  1 56 8.9 Python

  vembrane filters VCF records using python expressions

  

• gwas2vcf

  1 39 0.0 Python

  Convert GWAS summary statistics to VCF

  

• tronflow-vcf-postprocessing

  1 6 0.0 Shell

  A Nextflow variant normalization pipeline based on vt and bcftools

  

Vcf related posts

• Bam file genome viewing and whole chromosome plotting on a phone

  2 projects | /r/bioinformatics | 21 Mar 2023

• Convert VCF to MAF in Bioconductor?

  1 project | /r/bioinformatics | 9 Feb 2023

• We're wasting money by only supporting gzip for raw DNA files

  6 projects | news.ycombinator.com | 9 Jan 2023

• Help running hap.py

  1 project | /r/bioinformatics | 22 Nov 2022

• Has anyone stored/queried VCFs and their variant records in a relational database?

  2 projects | /r/bioinformatics | 12 Nov 2022

• AWS doesn't make sense for scientific computing

  1 project | news.ycombinator.com | 7 Oct 2022

• [TileDB webinar] Population genomics is a data management problem

  3 projects | /r/bioinformatics | 20 Oct 2021
• A note from our sponsor - InfluxDB
  www.influxdata.com | 14 May 2024

  Get real-time insights from all types of time series data with InfluxDB. Ingest, query, and analyze billions of data points in real-time with unbounded cardinality. Learn more →

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