AFAIK, the genome file along with its indexes are not needed during the genotyping step. Since we package hisat-genotype in a docker image using pre-built indexes, I'd like to keep the image as small as possible/avoid downloading these genome files every single time we launch a new instance. I've tested out the code using different use cases and removing that line seems to have no effects. Please let me know if there're other use cases that I haven't considered! Thanks again!
AFAIK, the genome file along with its indexes are not needed during the genotyping step. Since we package
hisat-genotypein a docker image using pre-built indexes, I'd like to keep the image as small as possible/avoid downloading these genome files every single time we launch a new instance. I've tested out the code using different use cases and removing that line seems to have no effects. Please let me know if there're other use cases that I haven't considered! Thanks again!