Benchmarking variants and comparing truth sets: List of useful tools and publications

Just realised that other than vcf-compare and bedtools intersect 

there's other options

 

https://github.com/RealTimeGenomics/rtg-tools

https://github.com/Illumina/hap.py

 

Also there's actually new variant callers ..

Molina-Mora, J.A., Solano-Vargas, M. Set-theory based benchmarking of three different variant callers for targeted sequencing. BMC Bioinformatics 22, 20 (2021). https://doi.org/10.1186/s12859-020-03926-3

 

Krishnan, V., Utiramerur, S., Ng, Z. et al. Benchmarking workflows to assess performance and suitability of germline variant calling pipelines in clinical diagnostic assays. BMC Bioinformatics 22, 85 (2021). https://doi.org/10.1186/s12859-020-03934-3

Additional file 23: File 3

. verify_variants.py

 

 

Zook, Justin M et al. “An open resource for accurately benchmarking small variant and reference calls.” Nature biotechnology vol. 37,5 (2019): 561-566. doi:10.1038/s41587-019-0074-6

Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`

hgvs.readthedocs.io/

• hgvs: A Python package for manipulating sequence variants using HGVS nomenclature: 2018 Update.

  Wang M, Callenberg KM, Dalgleish R, Fedtsov A, Fox NK, Freeman PJ, Jacobs KB, Kaleta P, McMurry AJ, Prlić A, Rajaraman V, Hart RK.Hum Mutat. 2018 Dec;39(12):1803-1813. doi: 10.1002/humu.23615. Epub 2018 Sep 5.PMID: 30129167 Free PMC article.

  • Sequence Variant Descriptions: HGVS Nomenclature and Mutalyzer.

    den Dunnen JT.Curr Protoc Hum Genet. 2016 Jul 1;90:7.13.1-7.13.19. doi: 10.1002/cphg.2.PMID: 27367167

   

• A Python package for parsing, validating, mapping and formatting sequence variants using HGVS nomenclature.

  Hart RK, Rico R, Hare E, Garcia J, Westbrook J, Fusaro VA.Bioinformatics. 2015 Jan 15;31(2):268-70. doi: 10.1093/bioinformatics/btu630. Epub 2014 Sep 30.PMID: 25273102 Free PMC article.
• VariantValidator: Accurate validation, mapping, and formatting of sequence variation descriptions.

  Freeman PJ, Hart RK, Gretton LJ, Brookes AJ, Dalgleish R.Hum Mutat. 2018 Jan;39(1):61-68. doi: 10.1002/humu.23348. Epub 2017 Oct 17.PMID: 28967166 Free PMC article.
• Clinical Implementation and Validation of Automated Human Genome Variation Society (HGVS) Nomenclature System for Next-Generation Sequencing-Based Assays for Cancer.

  Callenberg KM, Santana-Santos L, Chen L, Ernst WL, De Moura MB, Nikiforov YE, Nikiforova MN, Roy S.J Mol Diagn. 2018 Sep;20(5):628-634. doi: 10.1016/j.jmoldx.2018.05.006. Epub 2018 Jun 21.PMID: 29936258