Alternatives and similar repositories for seqr

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

• ga4gh / benchmarking-tools
  Repository for the GA4GH Benchmarking Team work developing standardized benchmarking methods for germline small variant calls
  ☆204Updated 4 years ago
• genome-in-a-bottle / giab_data_indexes
  This repository contains data indexes from NIST's Genome in a Bottle project.
  ☆256Updated last year
• atks / vt
  A tool set for short variant discovery in genetic sequence data.
  ☆201Updated 4 years ago
• PapenfussLab / gridss
  GRIDSS: the Genomic Rearrangement IDentification Software Suite
  ☆272Updated 3 months ago
• AstraZeneca-NGS / VarDict
  VarDict
  ☆198Updated last year
• broadinstitute / gatk-sv
  A structural variation pipeline for short-read sequencing
  ☆194Updated this week
• RealTimeGenomics / rtg-tools
  RTG Tools: Utilities for accurate VCF comparison and manipulation
  ☆325Updated 3 months ago
• WGLab / InterVar
  A bioinformatics software tool for clinical interpretation of genetic variants by the 2015 ACMG-AMP guideline
  ☆197Updated 2 years ago
• gatk-workflows / gatk4-data-processing
  Workflows for processing high-throughput sequencing data for variant discovery with GATK4 and related tools
  ☆156Updated 3 years ago
• Illumina / Nirvana
  The nimble & robust variant annotator
  ☆185Updated last year
• gatk-workflows / gatk4-germline-snps-indels
  Workflows for germline short variant discovery with GATK4
  ☆138Updated 4 years ago
• Ensembl / VEP_plugins
  Plugins for the Ensembl Variant Effect Predictor (VEP)
  ☆158Updated 3 weeks ago
• hall-lab / speedseq
  A flexible framework for rapid genome analysis and interpretation
  ☆317Updated 2 years ago
• brentp / vcfanno
  annotate a VCF with other VCFs/BEDs/tabixed files
  ☆383Updated 2 weeks ago
• dnanexus-rnd / GLnexus
  Scalable gVCF merging and joint variant calling for population sequencing projects
  ☆166Updated last year
• adamewing / bamsurgeon
  tools for adding mutations to existing .bam files, used for testing mutation callers
  ☆244Updated 11 months ago
• walaj / svaba
  Structural variation and indel detection by local assembly
  ☆246Updated last week
• lgmgeo / AnnotSV
  Annotation and Ranking of Structural Variation
  ☆262Updated last week
• bioinform / somaticseq
  An ensemble approach to accurately detect somatic mutations using SomaticSeq
  ☆199Updated last month
• counsyl / hgvs
  HGVS variant name parsing and generation
  ☆175Updated 2 years ago
• konradjk / loftee
  ☆180Updated 2 years ago
• hall-lab / svtools
  Tools for processing and analyzing structural variants.
  ☆154Updated 3 years ago
• Illumina / ExpansionHunter
  A tool for estimating repeat sizes
  ☆197Updated last year
• broadinstitute / mutect
  MuTect -- Accurate and sensitive cancer mutation detection
  ☆100Updated 2 years ago
• genome / bam-readcount
  Count bases in BAM/CRAM files
  ☆317Updated 3 years ago
• FRED-2 / OptiType
  Precision HLA typing from next-generation sequencing data
  ☆203Updated last year
• OpenGene / AfterQC
  Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
  ☆212Updated 5 years ago
• dkoboldt / varscan
  Variant calling and somatic mutation/CNV detection for next-generation sequencing data
  ☆163Updated 2 years ago
• zwdzwd / transvar
  TransVar - multiway annotator for precision medicine
  ☆126Updated 2 years ago
• PharmGKB / PharmCAT
  The Pharmacogenomic Clinical Annotation Tool
  ☆146Updated last week