Alternatives and similar repositories for doc-ANNOVAR

Users that are interested in doc-ANNOVAR are comparing it to the libraries listed below

• snakemake-workflows / dna-seq-gatk-variant-calling
  This Snakemake pipeline implements the GATK best-practices workflow
  ☆255Updated 2 years ago
• suhrig / arriba
  Fast and accurate gene fusion detection from RNA-Seq data
  ☆245Updated last week
• Magdoll / cDNA_Cupcake
  Miscellaneous collection of Python and R scripts for processing Iso-Seq data
  ☆271Updated last year
• BrooksLabUCSC / flair
  Full-Length Alternative Isoform analysis of RNA
  ☆232Updated last week
• dkoboldt / varscan
  Variant calling and somatic mutation/CNV detection for next-generation sequencing data
  ☆161Updated 2 years ago
• genome / bam-readcount
  Count bases in BAM/CRAM files
  ☆319Updated 3 years ago
• STAR-Fusion / STAR-Fusion
  STAR-Fusion codebase
  ☆243Updated last month
• WGLab / InterVar
  A bioinformatics software tool for clinical interpretation of genetic variants by the 2015 ACMG-AMP guideline
  ☆196Updated 2 years ago
• gpertea / gffcompare
  classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF
  ☆237Updated 3 weeks ago
• comprna / SUPPA
  SUPPA: Fast quantification of splicing and differential splicing
  ☆278Updated last year
• ConesaLab / SQANTI3
  Tool for the Quality Control of Long-Read Defined Transcriptomes
  ☆234Updated this week
• lgmgeo / AnnotSV
  Annotation and Ranking of Structural Variation
  ☆262Updated 2 weeks ago
• AstraZeneca-NGS / VarDict
  VarDict
  ☆198Updated last year
• rvalieris / parallel-fastq-dump
  parallel fastq-dump wrapper
  ☆299Updated 2 years ago
• PacificBiosciences / IsoSeq
  Iso-Seq - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads
  ☆217Updated 3 weeks ago
• pcingola / SnpEff
  ☆281Updated 5 months ago
• nf-core / methylseq
  Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel
  ☆169Updated this week
• bli25 / RSEM_tutorial
  A short tutorial on how to use RSEM
  ☆137Updated 5 years ago
• broadinstitute / gatk-sv
  A structural variation pipeline for short-read sequencing
  ☆191Updated this week
• gatk-workflows / gatk4-data-processing
  Workflows for processing high-throughput sequencing data for variant discovery with GATK4 and related tools
  ☆155Updated 2 years ago
• abyzovlab / CNVnator
  a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads
  ☆225Updated 3 years ago
• mskcc / vcf2maf
  Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms
  ☆392Updated this week
• bioinform / somaticseq
  An ensemble approach to accurately detect somatic mutations using SomaticSeq
  ☆197Updated 3 weeks ago
• bedops / bedops
  BEDOPS: high-performance genomic feature operations
  ☆345Updated 3 months ago
• mhammell-laboratory / TEtranscripts
  A package for including transposable elements in differential enrichment analysis of sequencing datasets.
  ☆255Updated 6 months ago
• igordot / genomics
  A collection of scripts and notes related to genomics and bioinformatics
  ☆214Updated 2 weeks ago
• ryanlayer / samplot
  Plot structural variant signals from many BAMs and CRAMs
  ☆544Updated last year
• nf-core / atacseq
  ATAC-seq peak-calling and QC analysis pipeline
  ☆207Updated 3 weeks ago
• ga4gh / benchmarking-tools
  Repository for the GA4GH Benchmarking Team work developing standardized benchmarking methods for germline small variant calls
  ☆203Updated 4 years ago
• PacificBiosciences / pbbioconda
  PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.
  ☆271Updated 6 months ago