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Table 2 Feature comparison of ExHap, GERMLINE and Sweep.

From: Congruence as a measurement of extended haplotype structure across the genome

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
  1. 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
  2. 1Initial "seed" "haplotypes" are exact match. After that, a user-configurable number of mismatches is allowed
  3. 2Segment-level details (shared between 2 chromosomes) can be aggregated to describe region
  4. 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
  5. 4Primary output is overlapping segments shared between 2 chromosomes, but report is at an individual level rather than chromosome level