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
  ☆154Updated 5 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 …
  ☆221Updated last year
• zwdzwd / transvar
  TransVar - multiway annotator for precision medicine
  ☆126Updated 2 years ago
• nygenome / lancet
  Microassembly based somatic variant caller for NGS data
  ☆155Updated 3 years ago
• CRG-CNAG / CalliNGS-NF
  GATK RNA-Seq Variant Calling in Nextflow
  ☆133Updated 2 years ago
• Illumina / Nirvana
  The nimble & robust variant annotator
  ☆182Updated last year
• macarthur-lab / gene_lists
  List of gene lists for genomic analyses.
  ☆222Updated 3 years ago
• cbg-ethz / NGS-pipe
  NGS-pipe: next-generation sequencing pipelines for precision oncology
  ☆111Updated 6 years ago
• ewels / AWS-iGenomes
  Documentation and description of AWS iGenomes S3 resource.
  ☆114Updated 7 months ago
• parklab / NGSCheckMate
  Software program for checking sample matching for NGS data
  ☆134Updated last year
• broadinstitute / gatk-sv
  A structural variation pipeline for short-read sequencing
  ☆189Updated this week
• geocarvalho / sv-cnv-studies
  Relevant papers for CNV and SV approaches
  ☆94Updated 8 months ago
• Ensembl / VEP_plugins
  Plugins for the Ensembl Variant Effect Predictor (VEP)
  ☆153Updated last week
• stevekm / IGV-snapshot-automator
  Script to automatically create and run IGV snapshot batchscripts
  ☆141Updated 2 years ago
• lima1 / PureCN
  Copy number calling and variant classification using targeted short read sequencing
  ☆136Updated 2 months ago
• zhanxw / rvtests
  Rare variant test software for next generation sequencing data
  ☆139Updated 3 years ago
• kundajelab / chipseq_pipeline
  AQUAS TF and histone ChIP-seq pipeline
  ☆109Updated 3 years ago
• ndaniel / fusioncatcher
  Finder of Somatic Fusion Genes in RNA-seq data
  ☆146Updated 2 years ago
• getzlab / rnaseqc
  Fast, efficient RNA-Seq metrics for quality control and process optimization
  ☆168Updated 8 months ago
• oncokb / oncokb-annotator
  Annotates variants in MAF with OncoKB annotation.
  ☆132Updated 3 weeks ago
• FRED-2 / OptiType
  Precision HLA typing from next-generation sequencing data
  ☆199Updated last year
• h3abionet / h3agwas
  GWAS Pipeline for H3Africa
  ☆110Updated last month
• dkoboldt / varscan
  Variant calling and somatic mutation/CNV detection for next-generation sequencing data
  ☆160Updated 2 years ago
• broadinstitute / ichorCNA
  Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.
  ☆185Updated last year
• atks / vt
  A tool set for short variant discovery in genetic sequence data.
  ☆199Updated 4 years ago
• bli25 / RSEM_tutorial
  A short tutorial on how to use RSEM
  ☆137Updated 5 years ago
• ryanlayer / giggle
  Interval data structure
  ☆233Updated 7 months ago
• CCDG / Pipeline-Standardization
  ☆82Updated 6 years ago
• mskcc / facets
  Algorithm to implement Fraction and Copy number Estimate from Tumor/normal Sequencing.
  ☆149Updated 2 years ago
• AstraZeneca-NGS / VarDict
  VarDict
  ☆198Updated last year