So sorry for my late reply. If I want to get primary contigs, should I set "--keep-haplotypes" option and "--no-alt-contigs" both; or just set the "--no-alt-contigs" option? You mentioned that “--no-alt-contigs” is used in default mode which may be different from haplotype mode using “--keep-haplotypes” option in my opinion.
Jerry-is-a-mouse
commented
2 months ago
So sorry for my late reply. If I want to get primary contigs, should I set "--keep-haplotypes" option and "--no-alt-contigs" both; or just set the "--no-alt-contigs" option? You mentioned that “--no-alt-contigs” is used in default mode which may be different from haplotype mode using “--keep-haplotypes” option in my opinion.