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