Secondly, we are working with .vcf files in GRCh38 build. Is there a way to run ALoFT using this build, or will we need to do a liftover back down to hg19?
Currently, ALOFT cannot be used with build38. We don’t have a plan to upgrade it to HG38. For SNPs, we already provide scores exome wide based on liftover to HG38. However, if you want other annotated features/scores for indels, it cannot be done without doing a liftover back down. While it is not ideal, that will work.