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1. oncoliner oncoliner Public

   A comprehensive benchmarking platform for monitoring, improving and harmonizing somatic variant calling across genomic oncology centers.

   Python 7

2. variant-extractor variant-extractor Public

   Deterministic and standard extractor of SNVs, indels and structural variants (SVs) from VCF files.

   Python 7 1

3. prepy-wrapper 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.

   Python 1

4. variant-callers variant-callers Public

   Scripts and containers to run the variant callers originally used in ONCOLINER

   Shell 3