Psst! I've posted some details about my notebook setup here.

Reproducible variant calling is possible with randomized algorithms

This morning I read On genomic repeats and reproducibility by Can Firtina and Can Alkan. The paper discusses two notable observations regarding calling genomic variants.

  1. Some sequence read aligners are not deterministic, and shuffling the order of the reads can result in different alignments.
  2. Some variant callers are not deterministic, and will report a different set of variants if an ...