Alternatives and similar repositories for loftee:

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

• davidaknowles / leafcutter
  Annotation-free quantification of RNA splicing. Yang I. Li, David A. Knowles, Jack Humphrey, Alvaro N. Barbeira, Scott P. Dickinson, Hae …
  ☆212Updated 9 months ago
• dkoboldt / varscan
  Variant calling and somatic mutation/CNV detection for next-generation sequencing data
  ☆156Updated last year
• stevekm / IGV-snapshot-automator
  Script to automatically create and run IGV snapshot batchscripts
  ☆140Updated 2 years ago
• bli25 / RSEM_tutorial
  A short tutorial on how to use RSEM
  ☆136Updated 4 years ago
• FRED-2 / OptiType
  Precision HLA typing from next-generation sequencing data
  ☆196Updated last year
• ENCODE-DCC / chip-seq-pipeline
  ENCODE Uniform processing pipeline for ChIP-seq
  ☆123Updated 5 years ago
• oncokb / oncokb-annotator
  Annotates variants in MAF with OncoKB annotation.
  ☆127Updated this week
• nygenome / lancet
  Microassembly based somatic variant caller for NGS data
  ☆154Updated 2 years ago
• kundajelab / chipseq_pipeline
  AQUAS TF and histone ChIP-seq pipeline
  ☆108Updated 2 years ago
• atks / vt
  A tool set for short variant discovery in genetic sequence data.
  ☆196Updated 3 years ago
• bmvdgeijn / WASP
  WASP: allele-specific pipeline for unbiased read mapping and molecular QTL discovery
  ☆103Updated 3 years ago
• freeseek / gtc2vcf
  Tools to convert Illumina IDAT/BPM/EGT/GTC and Affymetrix CEL/CHP files to VCF
  ☆147Updated last month
• broadinstitute / gatk-sv
  A structural variation pipeline for short-read sequencing
  ☆185Updated this week
• AstraZeneca-NGS / VarDict
  VarDict
  ☆194Updated last year
• im3sanger / dndscv
  dN/dS methods to quantify selection in cancer and somatic evolution
  ☆220Updated 2 weeks ago
• zwdzwd / transvar
  TransVar - multiway annotator for precision medicine
  ☆124Updated last year
• zhxiaokang / RASflow
  RNA-Seq analysis workflow
  ☆104Updated 3 years ago
• Ensembl / VEP_plugins
  Plugins for the Ensembl Variant Effect Predictor (VEP)
  ☆144Updated last week
• gatk-workflows / gatk4-germline-snps-indels
  Workflows for germline short variant discovery with GATK4
  ☆134Updated 3 years ago
• lima1 / PureCN
  Copy number calling and variant classification using targeted short read sequencing
  ☆132Updated last week
• geocarvalho / sv-cnv-studies
  Relevant papers for CNV and SV approaches
  ☆94Updated 4 months ago
• ndaniel / fusioncatcher
  Finder of Somatic Fusion Genes in RNA-seq data
  ☆145Updated last year
• kundajelab / atac_dnase_pipelines
  ATAC-seq and DNase-seq processing pipeline
  ☆165Updated 2 years ago
• suhrig / arriba
  Fast and accurate gene fusion detection from RNA-Seq data
  ☆235Updated this week
• jsh58 / Genrich
  Detecting sites of genomic enrichment
  ☆189Updated last year
• TrinityCTAT / Trinity_CTAT
  ☆116Updated last year
• VanLoo-lab / ascat
  ASCAT R package
  ☆177Updated last week
• secastel / phaser
  phasing and Allele Specific Expression from RNA-seq
  ☆112Updated 8 months ago
• snakemake-workflows / dna-seq-gatk-variant-calling
  This Snakemake pipeline implements the GATK best-practices workflow
  ☆250Updated last year
• CRG-Barcelona / bwtool
  A tool for bigWig files.
  ☆119Updated 6 years ago