Friday, 17 September 2021

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


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).


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).

Additional file 23: File 3




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`

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