as part of a project, I had to write an in-house pipeline to call germline mutations for ~100 patients.
For that I used Snakemake and GATKs best practice guidelines. Steps that take a long time (HaplotypeCaller or BaseQualityScoreRecalibration) are automatically parallelized over genomic intervals.
Furthermore, I tried to document the requirements to run the pipeline on your own as extensively as possible, and also included links, where to download gold standard reference material, so it is easy to use for people without a lot of experience.
I hope this is useful for anyone who is also trying to perform germline variant calling.
If you have any questions or improvements for the pipeline, please let me know.
You can find the project here: