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    5 repositories

    • variant-extractor

      Public
      Deterministic and standard extractor of SNVs, indels and structural variants (SVs) from VCF files.
      vcfvariant-callingvariant-analysis
      vcfvariant-callingvariant-analysis
      Python
      •
      MIT License
      •1•7•0•0•Updated Mar 6, 2026Mar 6, 2026

    • variant-callers

      Public archive
      Scripts and containers to run the variant callers originally used in ONCOLINER
      benchmarkingvariant-calling
      benchmarkingvariant-calling
      Shell
      •
      GNU Affero General Public License v3.0
      •0•3•0•0•Updated Jan 29, 2026Jan 29, 2026

    • oncoliner

      Public
      A comprehensive benchmarking platform for monitoring, improving and harmonizing somatic variant calling across genomic oncology centers.
      Python
      •
      Other
      •0•7•0•0•Updated Sep 17, 2025Sep 17, 2025

    • prepy-wrapper

      Public
      Wrapper for pre.py from Illumina's hap.py package. It is used to preprocess VCF files in order to normalize SNVs and indels for downstream analysis.
      genomicsvcfvariants
      genomicsvcfvariantssnvindel
      Python
      •
      MIT License
      •0•1•0•0•Updated Oct 17, 2023Oct 17, 2023

    • bioinfo-pipelines

      Public
      Bioinformatics pipelines to analyse whole-genome / whole exome sequencing data for tumors
      Dockerfile
      •
      GNU General Public License v3.0
      •2•1•0•0•Updated Oct 7, 2020Oct 7, 2020
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