Ivar, which oneroof uses for variant- and consensus-calling, currently doesn't support outputting multiple reference segments in consensus sequences. This is inconvenient for multi-segment viruses like H5N1 (not to mention for anything with chromosomes). Until the iVar team adds support, it might be worth writing a workaround that separates reads aligned to each segment into its own consensus-calling step and then remerges them afterward.
Ivar, which
oneroofuses for variant- and consensus-calling, currently doesn't support outputting multiple reference segments in consensus sequences. This is inconvenient for multi-segment viruses like H5N1 (not to mention for anything with chromosomes). Until the iVar team adds support, it might be worth writing a workaround that separates reads aligned to each segment into its own consensus-calling step and then remerges them afterward.