Alternatives and similar repositories for loftee

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

• freeseek / gtc2vcf
  Tools to convert Illumina IDAT/BPM/EGT/GTC and Affymetrix CEL/CHP files to VCF
  ☆162Updated 3 months ago
• davidaknowles / leafcutter
  Annotation-free quantification of RNA splicing. Yang I. Li, David A. Knowles, Jack Humphrey, Alvaro N. Barbeira, Scott P. Dickinson, Hae …
  ☆226Updated last year
• ewels / AWS-iGenomes
  Documentation and description of AWS iGenomes S3 resource.
  ☆118Updated last year
• ndaniel / fusioncatcher
  Finder of Somatic Fusion Genes in RNA-seq data
  ☆148Updated 3 months ago
• nygenome / lancet
  Microassembly based somatic variant caller for NGS data
  ☆154Updated 3 years ago
• lima1 / PureCN
  Copy number calling and variant classification using targeted short read sequencing
  ☆140Updated 3 months ago
• zhanxw / rvtests
  Rare variant test software for next generation sequencing data
  ☆141Updated 3 years ago
• CCDG / Pipeline-Standardization
  ☆82Updated 7 years ago
• h3abionet / h3agwas
  GWAS Pipeline for H3Africa
  ☆113Updated 6 months ago
• macarthur-lab / gene_lists
  List of gene lists for genomic analyses.
  ☆223Updated 3 years ago
• Illumina / Nirvana
  The nimble & robust variant annotator
  ☆188Updated last year
• AstraZeneca-NGS / VarDict
  VarDict
  ☆201Updated last year
• FRED-2 / OptiType
  Precision HLA typing from next-generation sequencing data
  ☆205Updated last year
• Ensembl / VEP_plugins
  Plugins for the Ensembl Variant Effect Predictor (VEP)
  ☆162Updated this week
• oncokb / oncokb-annotator
  Annotates variants in MAF with OncoKB annotation.
  ☆137Updated this week
• molgenis / systemsgenetics
  Generic Java genotype reader / writer, QTL mapping software, Strand alignment tool
  ☆176Updated last year
• parklab / NGSCheckMate
  Software program for checking sample matching for NGS data
  ☆136Updated last year
• geocarvalho / sv-cnv-studies
  Relevant papers for CNV and SV approaches
  ☆94Updated last year
• cbg-ethz / NGS-pipe
  NGS-pipe: next-generation sequencing pipelines for precision oncology
  ☆114Updated 6 years ago
• broadinstitute / gnomad_methods
  Hail helper functions for the gnomAD project and Translational Genomics Group
  ☆97Updated this week
• gatk-workflows / gatk4-germline-snps-indels
  Workflows for germline short variant discovery with GATK4
  ☆139Updated 4 years ago
• atks / vt
  A tool set for short variant discovery in genetic sequence data.
  ☆203Updated 4 years ago
• dkoboldt / varscan
  Variant calling and somatic mutation/CNV detection for next-generation sequencing data
  ☆165Updated 2 years ago
• mskcc / facets
  Algorithm to implement Fraction and Copy number Estimate from Tumor/normal Sequencing.
  ☆156Updated 2 years ago
• bioinform / somaticseq
  An ensemble approach to accurately detect somatic mutations using SomaticSeq
  ☆201Updated 4 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…
  ☆78Updated 5 years ago
• broadinstitute / mutect
  MuTect -- Accurate and sensitive cancer mutation detection
  ☆101Updated 2 years ago
• gagneurlab / drop
  Pipeline to find aberrant events in RNA-Seq data, useful for diagnosis of rare disorders
  ☆157Updated 3 weeks ago
• davetang / learning_vcf_file
  Learning the Variant Call Format
  ☆147Updated 4 months ago
• broadinstitute / ichorCNA
  Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.
  ☆192Updated last year