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

• dkoboldt / varscan
  Variant calling and somatic mutation/CNV detection for next-generation sequencing data
  ☆160Updated 2 years ago
• AstraZeneca-NGS / VarDict
  VarDict
  ☆198Updated last year
• broadinstitute / gatk-sv
  A structural variation pipeline for short-read sequencing
  ☆189Updated this week
• gatk-workflows / gatk4-data-processing
  Workflows for processing high-throughput sequencing data for variant discovery with GATK4 and related tools
  ☆151Updated 2 years ago
• lgmgeo / AnnotSV
  Annotation and Ranking of Structural Variation
  ☆260Updated 3 months ago
• shiquan / bamdst
  a lightweight bam file depth statistical tool
  ☆150Updated 9 months ago
• CCDG / Pipeline-Standardization
  ☆82Updated 6 years ago
• mozack / abra2
  ABRA2
  ☆92Updated 2 years ago
• snakemake-workflows / dna-seq-gatk-variant-calling
  This Snakemake pipeline implements the GATK best-practices workflow
  ☆254Updated 2 years ago
• genome / breakdancer
  SV detection from paired end reads mapping
  ☆117Updated 5 years ago
• parklab / NGSCheckMate
  Software program for checking sample matching for NGS data
  ☆132Updated last year
• atks / vt
  A tool set for short variant discovery in genetic sequence data.
  ☆197Updated 4 years ago
• stevekm / IGV-snapshot-automator
  Script to automatically create and run IGV snapshot batchscripts
  ☆141Updated 2 years ago
• walaj / svaba
  Structural variation and indel detection by local assembly
  ☆246Updated last week
• hall-lab / speedseq
  A flexible framework for rapid genome analysis and interpretation
  ☆317Updated 2 years ago
• BoevaLab / FREEC
  Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data
  ☆161Updated 10 months ago
• PacificBiosciences / pbsv
  pbsv - PacBio structural variant (SV) calling and analysis tools
  ☆152Updated 3 months ago
• ga4gh / benchmarking-tools
  Repository for the GA4GH Benchmarking Team work developing standardized benchmarking methods for germline small variant calls
  ☆202Updated 4 years ago
• PapenfussLab / gridss
  GRIDSS: the Genomic Rearrangement IDentification Software Suite
  ☆268Updated last month
• ndaniel / fusioncatcher
  Finder of Somatic Fusion Genes in RNA-seq data
  ☆146Updated 2 years ago
• gpertea / gffcompare
  classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF
  ☆230Updated last month
• PacificBiosciences / pbmm2
  A minimap2 frontend for PacBio native data formats
  ☆197Updated 3 months ago
• gatk-workflows / gatk4-somatic-snvs-indels
  This repo has been archived, these workflows are still available in the GATK repository under the scripts directory. The workflows are al…
  ☆77Updated 5 years ago
• OpenGene / gencore
  Generate duplex/single consensus reads to reduce sequencing noises and remove duplications
  ☆121Updated last year
• timflutre / trimmomatic
  Read trimming tool for Illumina NGS data.
  ☆138Updated 10 years ago
• nanoporetech / pipeline-transcriptome-de
  Pipeline for differential gene expression (DGE) and differential transcript usage (DTU) analysis using long reads
  ☆108Updated 2 years ago
• broadinstitute / gatk-docs
  Documentation archive for GATK tools and workflows
  ☆86Updated 5 years ago
• zwdzwd / transvar
  TransVar - multiway annotator for precision medicine
  ☆126Updated 2 years ago
• Griffan / VerifyBamID
  VerifyBamID2: A robust tool for DNA contamination estimation from sequence reads using ancestry-agnostic method.
  ☆97Updated last year
• gymreklab / GangSTR
  A tool for profiling long STRs from short reads
  ☆97Updated 4 years ago