Alternatives and similar repositories for gatk-docs

Users that are interested in gatk-docs are comparing it to the libraries listed below

• szpiech / selscan
  Haplotype based scans for selection
  ☆132Updated this week
• stevekm / IGV-snapshot-automator
  Script to automatically create and run IGV snapshot batchscripts
  ☆143Updated 2 years ago
• CenterForMedicalGeneticsGhent / WisecondorX
  WisecondorX — An evolved WISECONDOR
  ☆103Updated last month
• tobiasrausch / alfred
  BAM Statistics, Feature Counting and Annotation
  ☆150Updated last week
• 10XGenomics / supernova
  10x Genomics Linked-Read Diploid De Novo Assembler
  ☆65Updated 6 years ago
• AndersenLab / VCF-kit
  VCF-kit: Assorted utilities for the variant call format
  ☆130Updated 2 months ago
• parklab / xTea
  Comprehensive TE insertion identification with WGS/WES data from multiple sequencing technics
  ☆116Updated 3 months ago
• gencorefacility / variant-calling-pipeline-gatk4
  Variant Calling Pipeline Using GATK4 and Nextflow
  ☆58Updated 2 years ago
• gatk-workflows / gatk4-exome-analysis-pipeline
  This WDL pipeline implements data pre-processing and initial variant calling according to the GATK Best Practices for germline SNP and In…
  ☆55Updated 4 years ago
• KCCG / ClinSV
  Robust detection of clinically relevant structural and copy number variation from whole genome sequencing data
  ☆72Updated last year
• secastel / phaser
  phasing and Allele Specific Expression from RNA-seq
  ☆116Updated last year
• nh13 / DWGSIM
  Whole Genome Simulator for Next-Generation Sequencing
  ☆101Updated 10 months ago
• odelaneau / shapeit5
  Segmented HAPlotype Estimation and Imputation Tool
  ☆88Updated last month
• dnanexus-archive / parliament2
  Runs a combination of tools to generate structural variant calls on whole-genome sequencing data
  ☆103Updated 4 years ago
• Illumina / ExpansionHunterDenovo
  A suite of tools for detecting expansions of short tandem repeats
  ☆83Updated 2 years ago
• FelixKrueger / SNPsplit
  Allele-specific alignment sorting
  ☆59Updated 2 years ago
• odelaneau / shapeit4
  Segmented HAPlotype Estimation and Imputation Tool
  ☆96Updated 2 years ago
• genome / breakdancer
  SV detection from paired end reads mapping
  ☆117Updated 6 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
• geocarvalho / sv-cnv-studies
  Relevant papers for CNV and SV approaches
  ☆94Updated 11 months ago
• CCDG / Pipeline-Standardization
  ☆82Updated 6 years ago
• gymreklab / GangSTR
  A tool for profiling long STRs from short reads
  ☆99Updated 4 years ago
• dentearl / mafTools
  Bioinformatics tools for dealing with Multiple Alignment Format (MAF) files.
  ☆109Updated 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
• bmansfeld / QTLseqr
  QTLseqr is an R package for QTL mapping using NGS Bulk Segregant Analysis
  ☆81Updated 5 years ago
• BSSeeker / BSseeker2
  A versatile aligning pipeline for bisulfite sequencing data
  ☆65Updated 6 years ago
• tderrien / FEELnc
  FEELnc : FlExible Extraction of LncRNA
  ☆90Updated 2 months ago
• Griffan / VerifyBamID
  VerifyBamID2: A robust tool for DNA contamination estimation from sequence reads using ancestry-agnostic method.
  ☆99Updated last year
• BoevaLab / FREEC
  Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data
  ☆171Updated last year
• JimWhiting91 / genotype_plot
  A set of functions to visualise genotypes based on a VCF
  ☆87Updated 3 years ago