CRAM IO seems to be vastly faster when the reference genome is explicitly passed. These appears to be because an explicitly passed reference genome is trusted where a reference genome linked from within the file is validated to some extent
In MCHap, this means the reference path should be passed to each process that reads bam/cram files. It also means that an optional reference argument should be added to tools which don't currently require a reference genome.
timothymillar
commented
10 months ago
CRAM IO seems to be vastly faster when the reference genome is explicitly passed. These appears to be because an explicitly passed reference genome is trusted where a reference genome linked from within the file is validated to some extent
Relevant issues:
In MCHap, this means the reference path should be passed to each process that reads bam/cram files. It also means that an optional reference argument should be added to tools which don't currently require a reference genome.