Alternatives and similar repositories for gatk4-germline-snps-indels

Users that are interested in gatk4-germline-snps-indels are comparing it to the libraries listed below

• gatk-workflows / gatk4-data-processing
  Workflows for processing high-throughput sequencing data for variant discovery with GATK4 and related tools
  ☆159Updated 3 years ago
• dkoboldt / varscan
  Variant calling and somatic mutation/CNV detection for next-generation sequencing data
  ☆165Updated 2 years ago
• AstraZeneca-NGS / VarDict
  VarDict
  ☆200Updated last year
• broadinstitute / gatk-sv
  A structural variation pipeline for short-read sequencing
  ☆195Updated this week
• walaj / svaba
  Structural variation and indel detection by local assembly
  ☆249Updated 2 months ago
• genome / breakdancer
  SV detection from paired end reads mapping
  ☆117Updated 6 years ago
• shiquan / bamdst
  a lightweight bam file depth statistical tool
  ☆157Updated last year
• stevekm / IGV-snapshot-automator
  Script to automatically create and run IGV snapshot batchscripts
  ☆143Updated 2 years ago
• BoevaLab / FREEC
  Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data
  ☆172Updated last year
• ndaniel / fusioncatcher
  Finder of Somatic Fusion Genes in RNA-seq data
  ☆146Updated 2 months ago
• lgmgeo / AnnotSV
  Annotation and Ranking of Structural Variation
  ☆267Updated last month
• parklab / NGSCheckMate
  Software program for checking sample matching for NGS data
  ☆136Updated last year
• abyzovlab / CNVnator
  a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads
  ☆230Updated 3 years ago
• ga4gh / benchmarking-tools
  Repository for the GA4GH Benchmarking Team work developing standardized benchmarking methods for germline small variant calls
  ☆206Updated 4 years ago
• PapenfussLab / gridss
  GRIDSS: the Genomic Rearrangement IDentification Software Suite
  ☆279Updated 5 months ago
• OpenGene / GeneFuse
  Gene fusion detection and visualization
  ☆127Updated 3 years ago
• atks / vt
  A tool set for short variant discovery in genetic sequence data.
  ☆202Updated 4 years ago
• CenterForMedicalGeneticsGhent / WisecondorX
  WisecondorX — An evolved WISECONDOR
  ☆107Updated 2 months ago
• mozack / abra2
  ABRA2
  ☆95Updated 2 years ago
• abyzovlab / CNVpytor
  a python extension of CNVnator -- a tool for CNV analysis from depth-of-coverage by mapped reads
  ☆208Updated last month
• Illumina / ExpansionHunter
  A tool for estimating repeat sizes
  ☆199Updated last year
• genome / pindel
  Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants …
  ☆174Updated 5 years ago
• hall-lab / svtools
  Tools for processing and analyzing structural variants.
  ☆154Updated 3 years ago
• genome-in-a-bottle / giab_latest_release
  This repository contains information about latest release from Genome in a Bottle project
  ☆75Updated 6 years ago
• imgag / ngs-bits
  Short-read and long-read sequencing tools for diagnostics
  ☆168Updated this week
• zwdzwd / transvar
  TransVar - multiway annotator for precision medicine
  ☆126Updated 2 years ago
• adamewing / bamsurgeon
  tools for adding mutations to existing .bam files, used for testing mutation callers
  ☆248Updated last year
• suhrig / arriba
  Fast and accurate gene fusion detection from RNA-Seq data
  ☆253Updated last month
• bioinform / somaticseq
  An ensemble approach to accurately detect somatic mutations using SomaticSeq
  ☆200Updated 3 months ago
• OpenGene / gencore
  Generate duplex/single consensus reads to reduce sequencing noises and remove duplications
  ☆126Updated 2 years ago