Table 2.
Feature comparison of ExHap, GERMLINE and Sweep.
| Feature | ExHap | GERMLINE | Sweep/EHH |
|---|---|---|---|
| Requires phased chromosomes as input | yes | yes | yes |
| Handles missing data | yes | no | no |
| Allows small number of mismatches (fuzzy matching) | yes | yes1 | no |
| Designed to analyze a large number of SNPs (100 s to 1000 s) | yes | yes | no |
| Supports genetic distance | no | yes | yes |
| Outputs aggregate/region-wide metrics | yes | no2 | yes3 |
| Outputs chromosome level detail | yes | yes4 | no |
Seven features of starting data sets, algorithm logic, and resulting data are listed below. Each program is characterized based on the presence (yes) or absence (no) of the feature
1Initial "seed" "haplotypes" are exact match. After that, a user-configurable number of mismatches is allowed
2Segment-level details (shared between 2 chromosomes) can be aggregated to describe region
3Metrics are reported at a "core" level, where a core is a particular haplotype within a haplotype block. These metrics can be aggregated across all cores within a region to describe the region
4Primary output is overlapping segments shared between 2 chromosomes, but report is at an individual level rather than chromosome level