HiPhase v1.4.0

Changes

• Major changes to dual-mode allele assignment: Prior to this version, global realignment would revert to local realignment if the CPU cost (in seconds) exceeded a user provided threshold. While this was useful for fast-tracking noisy phase blocks, it could lead to non-deterministic output as CPU costs can vary. The thresholding has been reworked such that global realignment will revert to local realignment for an individual mapping if the edit distance exceeds a user provided threshold (default: 500). Additionally, global realignment will revert to local realignment for the remainder of a putative phase block if too many reads have reverted to local realignment (default: 50%, minimum number of failures: 50 mappings). This has the following downstream impact on results:
  • All results from HiPhase are fully deterministic from run to run.
  • Baseline quality scores for local realignment have been adjusted to scale at the same relative ratios as those from global realignment.
    • When running HiPhase on only small variants (e.g., local realignment mode only), this tended to slightly increase the number of switch flip errors relative to v1.3.0.
    • When running HiPhase on small, structural, and tandem repeat variants (recommended), we observed a small decrease in switch flip errors relative to v1.3.0.
  • Relative to v1.3.0, we observed reduced run-time costs for all tests (~25% reduction in both CPU time and wall-clock time, on average).
  • The number of mappings processed through global/local realignment are now tracked in the --stats-file.
• Global realignment is now on by default, reflecting our overall recommended usage of HiPhase. This can be disabled with the --disable-global-realignment option.
• CLI changes: The CLI has been updated to reflect the above algorithmic changes. These new CLI options have been added to reflect the changes:
  • --disable-global-realignment - This option will disable all global realignments; it is recommended if only small variant files are available for phasing
  • --global-realignment-max-ed <DISTANCE> - Controls the maximum allowed edit distance before reverting an individual mapping to local realignment (default: 500)
  • --max-global-failure-ratio <FRAC> - Controls the maximum allowed failure rates for global realignment before reverting the rest of the phase block to local realignment (default: 50%)
  • --global-failure-count <COUNT> - Controls the minimum number of failures required before the failure rate check is enabled (default: 50)
  • --global-realignment-cputime <SECONDS> - Deprecated, this option is now hidden on the CLI. It will produce a warning if used but has no impact on the downstream results.