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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