I have been using a modified version of the snakemake implementation of the GATK pipeline for genotyping. The pipeline first maps reads to the reference and calls variants per sample. Subsequently, variants are analyses jointly in a genotyping step. Now I want to run a new analysis workflow based in part on the same samples.
Is there a way to re-use the sample-specific rule results from previous analyses workflows such that they do not need to be recomputed? And what is the best practice for doing this; e.g. copying / symlinking data or using between workflow caching (can caching be done retro-actively) ?
Any advice is much appreciated. Thanks