Alternatives and similar repositories for gvcftools:

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

• brwnj / covviz
  Multi-sample genome coverage viewer to observe large, coverage-based anomalies alongside annotations and sample metadata
  ☆56Updated 3 years ago
• cc2qe / vawk
  An awk-like VCF parser
  ☆56Updated last year
• sequencing / NxTrim
  Adapter trimming and virtual library creation for Illumina Nextera Mate Pair libraries.
  ☆54Updated 6 years ago
• Cibiv / Teaser
  A tool to benchmark mappers and different parameters within minutes
  ☆44Updated 5 years ago
• jbelyeu / SV-plaudit
  Pipeline for structural variant image curation and analysis.
  ☆48Updated 3 years ago
• dillonl / graphite
  Graphite - Graph-based variant adjudication
  ☆28Updated 4 years ago
• vibansal / hapcut
  program for haplotype phasing from sequence reads and related tools
  ☆25Updated 6 years ago
• ljdursi / mergevcf
  Python package and routines for merging VCF files
  ☆29Updated 4 years ago
• lh3 / sgdp-fermi
  FermiKit small variant calls for public SGDP samples
  ☆17Updated 8 years ago
• tk2 / RetroSeq
  RetroSeq is a bioinformatics tool that searches for mobile element insertions from aligned reads in a BAM file and a library of reference…
  ☆65Updated 2 years ago
• kenchen / breakdancer
  SV detection from paired end reads mapping
  ☆38Updated 14 years ago
• jkbonfield / crumble
  Exploration of controlled loss of quality values for compressing CRAM files
  ☆34Updated 2 years ago
• lh3 / rtgeval
  Wrapper for RTG's vcfeval; DEPRECATED!
  ☆21Updated 9 years ago
• dantaki / SV2
  Support Vector Structural Variation Genotyper
  ☆58Updated 4 years ago
• aryeelab / umi
  Preprocessing tools for unique molecular index (UMI) sequencing reads
  ☆31Updated 2 years ago
• lh3 / htsbox
  My experimental tools on top of htslib. NOT OFFICIAL!!!
  ☆55Updated last year
• zeeev / mergeSVcallers
  heuristics to merge structural variant calls in VCF format.
  ☆36Updated 8 years ago
• cauyrd / ScanIndel
  The integrated pipeline for Indel detection
  ☆17Updated 6 years ago
• lexnederbragt / developments-in-next-generation-sequencing
  Developments in next generation sequencing: instruments, read lengths, throughput. See
  ☆27Updated 7 years ago
• rgcgithub / clamms
  CLAMMS is a scalable tool for detecting common and rare copy number variants from whole-exome sequencing data.
  ☆29Updated 4 years ago
• 10XGenomics / lariat
  Linked-Read Alignment Tool
  ☆27Updated 5 years ago
• Illumina / witty.er
  What is true, thank you, ernestly. A large variant benchmarking tool analogous to hap.py for small variants.
  ☆32Updated last year
• grocsvs / grocsvs
  Genome-wide reconstruction of complex structural variants
  ☆39Updated 2 years ago
• ryanlayer / stix
  Structural Variant Index
  ☆72Updated 4 months ago
• xuchang116 / smCounter
  smCounter: a versatile UMI-aware variant caller to detect both somatic and germline SNVs and indels. Published in article "Detecting very…
  ☆20Updated 6 years ago
• ALLBio / allbiotc2
  Benchmark pipeline for Structural Variation analyses, funded by the ALLBio.
  ☆24Updated 10 years ago
• benedictpaten / marginAlign
  UCSC Nanopore
  ☆43Updated 5 years ago
• tommyau / bamclipper
  Remove primer sequence from BAM alignments by soft-clipping
  ☆31Updated 5 years ago
• aquaskyline / 16GT
  Simultaneous detection of SNPs and Indels using a 16-genotype probabilistic model
  ☆27Updated last year
• lganel / SVScore
  Prioritize structural variants based on CADD scores
  ☆29Updated 4 years ago