A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

And a conceptual question: is there any reason why a pangenomics VCF (e.g. from <https://doi.org/10.1038/s41586-022-04808-9|this study>) wouldn't work well as a known sites file for BQSR?

So if I remember well from a collaboration I did with some bees people, more or less yeah

Basically to get a good known sites file, you do preprocessing and basic variant calling on a hundred of samples, and you use the resulting vcf as a known site, and you boostrap until the results are stable enough